does it matter if the amp is thx certified or not if using for ht while listening to either of the dolby formats?
No. THX certification only ensures that the manufacturer paid Lucasfilm engineers to verify that it meets certain performance benchmark standards set by THX to ensure it's up to at least minimum snuff. Besides the cert process, there's also a THX sound mode, which is to be avoided. My Integra receiver is THX certified, but I NEVER use the "THX" sound mode due to what it does (most notably changing the sub x-over freq to 80Hz), so I just use direct DTS (or whatever a movie is encoded in) or ProLogicII Music (sometimes Neo6 Music) if it's a 2ch movie/TVshow/etc source and I want to have surround sound. I prefer the Music versions cause they sound more natural to me than the Cinema versions of those soundfield settings.
Will my auddesy sound field from reciever still come through the amp?
As far as I understand it, Audyssey is an automatic dynamic eq thingie you use only after config changes, and as such should not be affected by this configuration. Your receiver was designed to biamp the main channels, so it should behave properly with the integrated eq feature. After you get your biamp wiring setup, listenn to it before and after going through the Audyssey eq process. It's possible that it is turning the gain on your mains lower than you prefer. If that's the case, after eq'ing it you can manually access the main channel's gain control in the receiver's menu and bump them up to your preference.
ps. what type of sub do you have, and what is your x-over set at?