I too am wondering why you can't lie on a bench. Can you be more specific as to why it is uncomfortable?
What should make it more comfortable is adding more risers. Your height chiefly determines how many risers to use (e.g. I tend to only use 1 each side or I really have to work super hard to keep my lower back down on the bench.) So try three for starters. Maybe four if you need it ...
As for muslces, you should be feeling it in your chest, with probably a little in the shoulders though we try to limit that by pulling the shoulders down and away from the ears.
Elbows should not dip below the top of your bench.
Make sure you have the right target zones though. Elbows should be out, bar travels down to the chest (or nipple line.) Get your instructor to check for you, that's what they're paid for.
If you're doing it all well, though, and you're sitll not feeling it, time to add weight 
Free the body.
The mind will follow.