They say not to carry the yarn for more than 5 stitches. That's why Fair Isle patterns don't include big areas of one color, because the other color would need to be carried too far.
You won't have a lot of ends to weave in if you use the intarsia method. You will need a strand/bobbin of yarn for each color section. It sounds like you only have a few color sections, so that's not too many ends to weave in.
Hope that helps! Happy knitting!
KnittingHelp Queen Bee
It is not because things are so difficult that we do not dare; it is because we do not dare that they are difficult.