You should use DD/DTS with that setup.
Use prologic if you prefer when you have a stereo source. With a Multichannel source, having discrete channel information for your speakers will be a much bigger difference than using PCM and only getting 2 channels + pseudo surround.
From my research and personal experience, going from DD/DTS to the HD audio formats is not nearly as big a deal as some people make it out to be.
Here's as close as I've found to a double blind article on comparing the DD/DTS to lossless formats
http://www.hedmag.com/node/Dolby_TrueHD_DTS-MA_versus_Uncompressed_PCM
On Dolby's own reference system / room, they had a hard time telling the difference in short clips tested several times back to back.
There are probably huge issues with your system that need to be resolved that would make much bigger differences than the improvement you'd find going from DD/DTS to the HD audio formats that you're not able to get now.
Having Audyssey in your receiver is probably making a big improvement for the system. Optimizing room placement, attacking any acoustic issues with room modification, getting multiple subwoofers, upgrading speakers, etc. are all probably going to be bigger differences in your sound than getting the lossless audio tracks.
I don't want to call anyone a liar if they think that the new HD audio formats are a huge difference. There are a ton of people out there who do think that there's a huge difference. Keep in mind that there are a lot of variables in comparing the two, and without asking about how they actually compared the two, the conclusion could be very misleading.