There are a couple of methods I've seen used ... despite what Chris Schwarz says I prefer using a countersink to remove a slight bit of metal.
IME it's quicker and easier.
But to be fair, I'm not that OCD that I've done it more than once/twice just to see.
Personally I find it looks wonky in the end product to have the screw heads at different levels; despite the slots being "clocked".
Further, I rarely use slotted screws; which to my eye would are most noticeable un-clocked.
I've had success in the past over/under tightening screws but never felt the hinge was properly installed when doing so.
Here's his take on it:
http://www.popularwoodworking.com/woodw ... crew-heads