If you don't mind loops on the edges from carying the yarn up the rows, it shouldn't be too bad. You just want to make sure the yarn will be on the correct side when you're getting ready to pick it up again.
If you're using wool, or another animal fiber, you could felt the ends together carefully so the yarn will remain in one piece at each color change. There are videos for that on the site here...
If I were doing the same, I'd probably cut the yarns and have a million ends to sew in, just becasue I like neater edges.
As for sewing up, you may want to use the apropriate yarn for the aproriate color; just weave up carefully on the cc so it doesn't show or get loopy
Hope that makes any sense... It's almost not to me as I go back and read it.