First, let me say that what works for one person doesn't necessarily work for others, especially when you're talking about scopes. Cheek weld, eye relief, etc. etc all come in to play. Here's what I eventually settled on, and it works perfectly for me; but may not be for everyone.
I wanted to keep my BUIS (because I still don't trust scopes totally); but be able to use my Aimpoint Comp2/M68 and also my Leupold VX-1 3-9x40 scope. When I first got my flat top, the Aimpoint was fine; but I had to take off the BUIS for the Leupold to be mounted. No good. I bought a RRA 5/8" riser, and everything was good to go:
Flat top with riser. The BUIS still clears the riser and can be used if all the scopes go to hell in a handbasket.
Riser with Aimpoint. It raises the Aimpoint to where I don't get co-witness; but that's not really a big deal. I prefer my head up a little for combat shooting anyway--it's the way we were trained to do it in the 80's with iron sights (and hence my saying that my way is perfect for me; but may not be for everyone);
And finally with the Leupold. I just fold down the BUIS, and it's ready to go. I use Warne quick-detach High rings for this, and they work great. (I also use them on a scoped Garand--in .30-06--and they never lose zero!) The scope is Leupold VX-1 3-9x40 (around $220), with Butler Creek lens caps.
Since the Aimpoint and the Leupold are both quick-detach, I just leave the riser on the weapon since it doesn't get in the way of the iron sights.
So, hopefully you can get some ideas from this set-up and maybe get something that works for you.