Don't have Atmos myself but from what I've gathered around here is that having your surrounds and rear surrounds in the ceiling will negate the effects of another set of ceiling speakers for the Atmos channels. Can you not bring the surrounds down to at least in-wall positions?
Yes some avrs have more processing channels than amp channels so read descriptions carefully; those that have 7 channels of amps but 9 channels of processing (or 9 and 11, or 11 and 13 etc) will require an external amp to fill the gap. Zones aren't for this purpose, that's for another set (or 2 or 3) of stereo (L/R channels) speakers in other rooms; you need the proper number of amp/processing channels you want in the main zone (which is normally what they show as a feature). Additionally using zones if you've maxed out any built-in amp options (which for a 3rd zone may not exist in the avr at all) will also require external amps.
Citing number of drivers (i.e. 3 way) and a wattage rating don''t tell us much....better to cite specific make/models of speakers for advice as well as your desired listening levels; nominal impedance can be helpful for matching to avrs but keep in mind the speaker's rating is just that, a nominal rating (the impedance changes with frequency both above and below a nominal rating),and they're not always correctly rated either. Speaker sensitivity is a useful spec, tho.
