I alternate every other row working flat, and every round working in the round. For my sweater above, I’m alternating every round for the body, but didn’t alternate on the sleeve and you can see it’s slightly darker/more blue than the body. I don’t mind if the sleeves vary a bit from the body as long as they match each other. Switching frequently is usually the easiest, since you don’t have to worry about counting rows between switches or carrying the yarn up evenly, and it’s the most even blend.
On the other hand if you don’t want to manage two balls of yarn the whole time, or if you want to use up one skein completely so you only have one partial leftover, you could knit up most of the first skein, then join the second and alternate until you run out of the first. You’d get more of a gradient/fade effect, but still looks nicer than an abrupt shift. I’d say the more the two skeins differ, the sooner I’d want to join the second to get a longer blended section.