Gotta figure it's instinctive, just like how Ben can usually figure out a new alien's powers almost immediately.
I agree with Silentia, he probably just moves as and uses any new aliens powers by instinct.
well it wouldent be his own moter skills the omnitrix would has had to put them in for him unless he was working it out off camera. also wouldent upgrade need to constantly make new moter skilles when he merges because his body is in a diffrent shape.