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!