Hi,
If I have collected a 10 % Payment in Advance how do I subtract that amount in the Final Invoice?
Less Deductions
or Advance received etc.
Thanks and regards
Marcello
Read the Guide about customer advances.
Welcome to the forum 
The guides that @Tut is referring to can be found here (recommend you bookmark them):
As for the specific guide he mentioned about customer advances, you can find that here: