Background: lifted a lot through high school and college, mostly high rep stuff with no real program or discipline. After college quit working out all together with work and whatever. Fast forward 10 years. I get into starting strength and do that for 6 months, injured my shoulder, quit lifting. A year later, here we are.

I've got 2 squat racks, incline/decline/flat benches 4 barbells, 4 sets of 300lb plates, dumb bells up to 100lb. Shoulder is letting me do body weight dips and overhead press so far..

The girlfriend has always been a health nut, she just moved in and expressed interest in lifting heavy. She read my starting strength and 5/3/1 books and is on board. Which is gonna make this a lot easier to have an accountability partner in the house making me dinner.
We downloaded 5x5 apps did our maxes and have been doing it for a couple weeks. Going well.

On to the question: we need some accessory chest/arm/calf etc work -basically bro lifts I guess Any recommendations on lifts using the equipment we have? And most importantly, how many reps and sets and which lift days do we do them?

P.s. we have the extra app add on for 5x5 accessory work and want more.. mostly worried about which days I should do, for example, fly's and tricep work so we don't hurt core lifts. Do then after core lifts on same day as bench??

You can do them after the core lift or on opposing days. To be honest accessory work placement doesn't really matter as long as it isn't interfering with your main lifts. I'd personally pair it up on a different day for the lifts that you can and for the ones that you can't just do it after the main lift.

I'd keep your assistance simple for now. I'd hit 3 sets of curls, 3 sets of some sort of tricep extension (overhead, kickback, etc), a few sets of flies, and a few sets of lateral raises a couple times a week. Don't feel good? Skip the accessory stuff al together. Feeling fantastic? Throw some in that day. Stalled? Dump the accessory work.

HOWEVER, if I were in your shoes I'd probably just not do any of it for now. Stick to the program as written and when you stop progressing switch to 5/3/1 and pick whichever one of Jim's many templates suits you best (Boring but big and triumvirate are nice). The assistance work won't make you or break you at this point so if I were you and I was still progressing on main lifts I'd just ride that out and try not to mess with it.

I think the Starting Strength book has some accessory stuff in there, doesn't it?

So 5x5 you are doing Squat, Bench, Military, Bent Over Rows, and Deadlift right? ABA BAB schedule?

For Bench Press some of the accessory excersizes you could do include Dumbell Bench Press or Dumbell Chest flys. You can also do skull crushers for tricep work. You can also do dips, and DB kickbacks.
For Deadlifts you can do stiff legged deadlifts or Romanian deadlifts.
For squats you can do good mornings, Dumbell lunges.
For Military Press you can do Dumbell overhead press, you can also do Dumbell Lateral Raise or Front Raise.
For BOR you can also do pullups, lat pulldowns, bicep curls ...

For accessory work I believe they want you to do 3 sets in the 8-12 rep range. Not as heavy or intense as your main lifts.  Try to hit the same muscles from a different angle, or with dumbells instead of barbells.

ETA: Looks like Pancake of Doom already did a good job answering it.
My personal opinion is I do associated accessory work after the main lifts on the same day. This maximizes my recovery time for those muscle groups. YMMV. I feel like if I do too much on my off days than I don't really get sufficient recovery.

I try to just throw some bicep stuff in here and there.  It doesn't take long.  The best bicep workout is neutral grip weighted pull-ups.  Yeah you can go do the curl bar, but that's not putting 300# of pressure on your biceps.  Also can do weighted chin ups.  

Triceps, I like skull crushers.  Also weighted dips, but those tend to hurt in various places.  And I concentrate on a narrow grip bench, which also builds triceps.

eta:

if you want to do calves - I'm not convinced it helps all that much - I would just load up a barbell like you're doing a really heavy back squat and just do calf raises.  I don't even use blocks - just off the ground.  You can do calves every single day if you want to probably.  IMO though, you have to push the weight on calves rather than just doing a zillion reps.

I liked flip flopped BBB.

Good info guys. Thank you

Pull-ups (weighted if possible)
Face pulls
Rows (one armed)
Pull aparts
Curls (you biceps WILL be used in pressing movements)
dumbbell presses
RDLs
Front squats or leg presses
Shoulder rotator work

After I do 3x5 on squats I drop the weight and do 3x8-10 on them for some leg pump action. After 3x5 deadlifts I do heavy rows and weighted pullups (pronated grip), then neutral pullups with bodyweight and some ez curls to finish, usually with girl weights because I'm fried at that point. After 3x5 on flat bench and OHP I've been doing reverse grip bench around 3x8 and bodyweight dips, then tricep pushdowns to finish.

I'm doing a PPL now though, so I have 4-5 days before repeating a big lift and the associated accessories. If I was squatting every other day I think that plan would lead to burn out. Every time I try to go back to full body I end up not liking it and have to go back to bro'ing out a bit.

Once work starts up again I'll probably stick to a Deadlift/Row/Pullup day and Squat/Bench/OHP on a 3x week schedule and drop the accessories, but work destroys me in the spring, I have to put more energy into making money than making gainz.

Which ones?

I get a lot of anterior delt DOMS from hard pushing days, and it can feel like the top of the bicep, but it isn't.

Funny how people are different. Dips don't be bother me at all but skullcrushers hurt my elbow.

Same with me, I could do dips every workout, rings or bars. Skullcrushers even with an empty bar kill my elbows.

I guess dips are harder on your body when you're a deep heavy six.  

Biceps are the brakes in pressing movements(lats too). I never really notice my biceps until I get above 365 on bench, but once I get up there I am glad I have big arms.

When you say you are getting all that soreness from hard pushing days, is it from overhead work? If you are getting it just from benching I would recommend spending some time 1) working on your bench form and 2) doing some dedicated shoulder work and hit all 3 heads.

I try to press in every direction on a push day, or make it even with full body days.

Right now I will flat bench, OHP and dips on the same day.

My flat bench, even with a retracted scapula has a lot of activation in the delts, they aren't delt dominant, but they are working hard. OHP seems to hit front and medial, my dips are very chest dominant.

On bench, you may want to try touching a little lower, make sure at the top the bar is straight over your shoulders(not above over your neck or face), and tighten your elbows a bit. Obviously we are all built different, but benching should not be hard on the shoulders. Guys who bench in a way with a lot of delt activation tend to be the guys that say "I used to be able to..."

It's not hard on them at all.

When I first started doing it I ran into pain with it. I had to basically start over and focus on form.

Retracted scapula, bar path experimentation, controlling the elbows (ego got me the first time around and I was doing everything wrong to move more weight). It gives me zero issues now, it just isn't a 100% chest and tricep movement for me, there is always delt work with it, and I think because I used to do so many dips they ended up lagging behind, which is why the get sore more often than the chest does.

Why do you think you need accessory lifts?

I'm barely familiar with 5x5 but if I remember correctly, you start out really light. Once you progress to heavier weights, any extra work will impede your linear progression.

LP programs are meant to be relatively short term to capitalize on newb gains. I see no reason for accessory lifts (other than chins) until you are an advanced novice/intermediate.

You've got a good point.. I hadn't really thought of it like that