Here's what I tend to do.
Say you want to twist one of the centers. Put said center on the top layer. Use a <U,U',U2> move to put it in its right spot. Then do an M'. Then undo the first move you did, and then do M. Repeat until the cube is restored (you'll need to do it 3 times for U2, but 6 for U or U').
E.g if the center on the top needs to go counter clockwise, do U' M' U M 6 times.
Then, just repeat all of that for all the centers that need to be twisted!
Hope this helped.