The main thing on a multi-colored project is to make the outside look good. On the inside you're twisting st, attaching different colors, weaving in yarn, etc. You can do you best to keep it simple on the inside--keeping any loops small, etc.
If you are alternating colors, as in Fair Isle, being consistent helps to make the inside neater. Always designate one yarn as your "top" yarn and one as your "bottom" yarn. As you bring them across the back along the row be consistent as to which yarn is above the other. It's very hard for me to explain, I hope you have something on two-color knitting. If you have a specific problem, please share. Hope this helped