So I'm having a lot of pain when I'm trying to shoot in the prone position. I'm getting a very nasty bruise from just a 308 right now above my collar bone. Was watching some Youtube vids and noticed that a lot of precision shooters are placing the buttstock low, almost on their pec. Just curious how you should hold the rifle to avoid bruising and enjoy this a lot more... Do you place the stock below the collar bone or on it?

You put it where you put any rifle, in the shoulder pocket, which is bordered on one side by the collarbone.

FWIW, A trick another shooter and I were discussing a couple weeks ago was to get a not too thick but nice and firm pillow under your trigger-hand elbow. That has the net effect of opening your shoulder pocket a bit so it's easier to fit a buttstock pad in it without it crossing onto bony stuff and keeps your elby-bone from getting rubbed raw on the ground. I've used this method in 1 match so far (hey, we just came up with it a few weeks ago) and so far it's helped. My elbow has skin on it and my .308 didn't beat me up nearly as bad as it usually does. Was still sore at the end of 50rds but not tender to the touch sore like last time.

Could also do what I prefer, shoot a .223, those never hurt. I'd be shooting one but my cerakote guy is taking his sweet damned time and I don't have my .223 barrel on hand.

Get a slip on LimbSaver and/or a brake...or put up with it.

My 230gr .308 load has the recoil of a 30.06, with a LimbSaver and brake I can shoot 100 rounds plus another 100 rounds of 140gr 6.5G in a few hours time with zero recoil issues.
Both have brakes and decent recoil pads. Stock is on my collar bone as rob described.

The lower end of the butt plate (the "toe") goes in the pocket.  The pocket is the hollow spot between the deltoid, the pectoralis and beneath the outer end of the clavicle (collar bone).

At some point, you may find you prefer it somewhere else because that other place provides higher scores.  It is a starting point.

Adding the APA little Bastard brake on my .308 was a huge improvement. My shoulder would be stiff after 50 rds... now, It's like shooting my AR's...

I highly recommend a brake.

Okay.  So I was dealing with the same issue.  I found the true fix.

Taller rings.  

Many of the videos you are seeing have the scope mounted higher because of the large objective on the scope.  The side effect of the taller rings, you have the rifle mounted under the collar bone.  Of course you need a riser of sorts on the top of the stock.  

I went to taller rings on my bolt gun (a 270WSM in a Boyds laminate) and it is easy to shoot prone now.  My Remington R25 has always been a light kicker (308Win) because of the design but with taller rings I can keep my head down and see the impact which I was never able to do before.  The R25 (AR10 family) does not require a riser on the stock like the bolt gun.

I saw a video of a brake on a 300 WM that really impressed me made by HB Tactical in PA.  They make a lot of other brakes as well and I am in no way associated with this company.

Agreed, that is what I have on my .308, plus the LimbSaver, plus the rifle weighs 17lbs.

Though I just got a LabRadar, I have read that the APA Bastards are the worst for concussion on the unit. I'll be interested to see how it works this weekend, hope there isn't an issue.