I have tax levy And my employer has been taking out a certain amount each paycheck. Will they deduct this amount from my FICA with holding on my W2?

Levies happen "after tax", the same as if you got your regular paycheck, then you wrote  check out if it for the amount of levy.  FICA is not adjusted, you still pay that on the levied amount.

So on my W2 the FICA with holding should be the same as on my paycheck stub?

Not necessarily....some employers combine the social security and Medicare together on a check stub, then its broken into the proper categories on the W2.   A W2 doesn't have a box for FICA, it has Boxes for SS and Medicare, which together make up "FICA".