Zones are setup to emulate physical boundaries. So if you have two IP phones physically isolated on the network, then you may want to put them in their own zone, and enable compression between that zone and any other zone. That would mean that when a call is made to/from one of those phones, compression will be the preferred codec.
As for licensing. The IP phones carry their own, so calls between them can be compressed (based on the zones) and they will not count against your system compression licenses. The compression licenses that you purchase (and require the system DSP support to use) are for any IP calls who's leg _terminates_ on the controller. The controller is defaulted to Zone 0 (or is it 1?), regardless it's the first zone. Depending on the zoning rules you have setup, compression is applied based on those rules, just like if an IP to IP phone call was being made.
I say "who's leg terminates" because it's not isolated to PRI/TDM trunks, it also applies to IP phone legs into a conference, an IP phone using MOH, or a group page. Any case where an IP device is streaming to the controller.
Hope that helps.