In Magic in the Shadows it gives rules for stacked foci, but they really only focus on making them. My first question is what about attacking them from the astral plane. Can you single out one of the foci or do you have to attack the entire foci. An example: if I have a stacked two sustaining focus 4/4 does it count as attacking a force 8 focus or could I only attack on of them? Also, when using the rules for focus addiction, would you only count the amount of the focus you used? Again if you only sustained one force 4 spell, but not the other, would that count as using a force 4 foci or a force 8?

Stacked foci are only stacked in their powers. Having a stacked foci lets you include the powers of a spirit focus and a spell focus for example. No matter how many powers you stack into a focus it is still one focus and so must be attacked as one focus. Activated stacked focuses activate all levels of the stack so effectively your example is a force 8 focus.

But do foci you have active count as using them even if you don't use the dice offered from a foci?

Yes. Otherwise, foci that don't provide you dice (such as sustaining foci) would never count against the total.