When I pay my federal with Turbo tax is the self-employment tax included?....seems like one option pays too much, the other not enough

Hard to tell if I'm asking a silly question, but started an new business this year and as expect, it was a little soft....when I go through TT, I come up with 

Federal Due, about $3800

Self Employment Tax, $3650.

When I pay the $3800 is that including the $3650?  I never get prompted to pay the self-employment part separately, but paying both would seem higher than what I'd expect to pay, paying just one seems like not enough.  I read the stuff about half of the self-employment being deductible---which makes it even more unclear.  Just need to know if I need to make separate arrangements to pay the rest.