As JD noted above (and as is explained in the beginning of this thread where models are compared), you would need to step up to the X3000 to get bass/treble adjustments for Zone 2 speakers. The Zone 2 output of the X2000 is simply an unprocessed line level output, so no setting (Audyssey, DEQ, tone controls, etc) will impact the sound quality.
That said, I don't agree with the poster above that you simply have to accept the poor sound quality as an inherent consequence of your speaker choice. You do have another option, that is to utilize the Zone 2 pre-outs and feed the unprocessed line level output to another preamp which can provide the audio controls you need. For example, find a cheap stereo receiver used at a garage sale or local criagslist (should be able to find one for $20-50 max) and then input Zone 2 via the pre-outs to one of the RCA inputs on the stereo receiver. Then, use the stereo receiver to tailer the sound quality using the bass/treble and other options. If you want to get a little friskier, you could even try to find a cheap used receiver with Audyssey and DEQ that would enable you to run a calibration on those Zone 2 speakers, although obviously that would cost a bit more (although I see older units like the AVR 590 go for $100 all the time).
Thanks very much for the suggestions Batpig and Chi-Guy! Thats great news, this is something I will attempt this week. Just to clarify the connection setup, I am assuming I still power the speakers from the zone 2 connections on the X2000, then connect via RCA cable the speaker output from the stereo receiver to the zone 2 pre-out?