I just put a 3x9 bushnell scope on my Bushmaster M4, do I still zero at 50 yards like iron sights?

Depends on the height above bore of the scope.  If the centerline of the scope is at the same height as your irons, then it should be the same.  Given that there are varying mounts that can change how high the scope sits, I'd recommend zeroing it at 50 and then checking it at 200, if possible, and seeing where you're at.  If nothing else, zeroing at 50 will get you in the ballpark.

Depends

but I do like Chucks 50y zero for my SHTF M4`s


I ran a Bushnel 3.5-10x on my Bushmaster A1 20 inch hbar
Sold the Rifle but kept the scope

Depends on what you intend to do with your rifle?

Since you mounted a 3x9 scope on your rifle, I assume you do not intend to use it for CQB (or self defense around the home).  If you intend to shoot coyotes or prairie dogs, you might be better off with a 40 yard (200 yard) zero (as opposed to the 50 yard (100 yard) zero normally suggested for self defense).  If all you intend to do is punch paper, why not zero it for the range you normally shoot paper at?  

As (or if) your intended uses change you can always change the zero.

Paper (maybe cats at the slaughter house, shhh)...but id like to get a range where i can easily adjust POI for 50,75,10,150,200 meters

This is why I like BDC reticles. One trip to the range and you can figure out your different POI's real quick.

I had a Burris FF II 3-9x on my RRA entry tac and zeroed it at 50yds, knew I'd be a couple inches high at 100, 2nd mark was 200yds, between 2nd and 3rd mark was 300yds. I was ablke to shoot out to 300yds like this quite well, esp considering it's a service grade carbine!

On my 3x9.. I zero @ 50



10yds is about 2ish" low

25yds will impact 2" low

50yds is zero

100yds will impact 2" high

200yds will impact about a .5"high to zero.