[COLOR="#330099"]You can use your favorite join method or pick one that seems to fit. Amy shows several joining techniques her on KH knitting tip page. Scroll down to the joining section.
Since true Fair Isle uses only two colors in any one row (well you could sneak in a sparse, third color using intarsia) you will likely be dropping one color and picking up the new one.
I prefer what she calls a double knit-in join to prevent holes. A duplicate stitch join would work as well and may be easier. I just dislike weaving ends in later as I'm just as likely to forget. :roll:
You can also make the change in the unused color during a 3 stitch or longer float.
Fair Isle has three positions for yarn: 1) Used in the stitch, 2) float behind stitches 1 or 2, or 3) wrapped in by stitches 3 or 4. By using stitches 3 and 4 you can alternate the unused color that is wrapped and secure by the stitch. (The stitch numbering is the same as that used by the Philosopher's Wool video.)
No sure I could make the muddier or not.