Rubik's Revenge (4x4x4x) original method Step3. Inners at top layer. Now you made four columns. You can position inner cubes at top layer using r,l,u,d,f,b, and U, D layers.
ex. a->*: dr'd'r or b'rb, b->*:
bDr2b'
STEP1-2
STEP3 STEP4 STEP5 STEP6 STEP7

If you use only these layers, you never mix your four columns.
If
possible, I make a pair of inner cubes in middle layer, then position it.