I've only done two colors of fair isle in the round and in my case I knit with two hands when I'm doing it so I keep the yarns on each side of me.
I've been doing 4 color striped hats and I keep the balls in a row next to me and move them up one at a time to knit the next color.
I've not done intarsia so I can't say from experience. I've heard that the bobbins get twisted though. Some people just leave a longer yarn dangling for each color rather than put them on bobbins. It may mean a few more ends to weave in because you can't make them too long, but it sounds preferable to me.