Switch power supply, how to choice frequency?

Ideally, the two parts will run at frequencies that are related. You don't want them to slowly drift past each other. This tends to make a low frequency ripple on the output that is hard to remove.

Both sections have a comparator in them that does the timing. You want to avoid having either sections power switch change state right at the time that the comparator is about to make the edge. There will always be some noise from the transistor switching and you want to keep this from effecting the timing of the other section.

Beyond these considerations, the two frequencies are determined by the needs of the two sections either may be the greater of the two or they may be equal.