It is irrelevant which part of a figure is selected when you save a pose. If you want to save a partial pose you can use 'Select Subset'. No pose data is saved for the BODY actor in versions prior to P7 (where it is an option).

I think I saw a python script to save poses that include BODY data, but I can't remember where.

If you want to exclude some actors from pose at the time you apply it, you can lock those actors, after applying the pose the actors can be unlocked again. It's handy to have some lock/unlock poses for the lags, arms, hands-fingers, head,  and especially the eyes.