Audyssey can be rather hit and miss sometimes.
Best thing to do is to run an auto setup and save it, from there you can change and tweak, then resave as and when you need to. After you've ran the auto setup, use a tape measure and check the distances are correct that have been set for the speakers. If you have a sound meter handy you can also check levels. I tend to add 1dB to the centre speaker after set up. Getting the sub level right is the hardest. This can't always be done accurately with a level meter. I tend to leave it on the volume level the auto setup has set, then twek up or down (usually down) over a period of a few films to get an idea of where it should roughly be set.
One thing that will hugely affect how the system sounds is the crossover frequency. With 2005's, I'd cross them over at about 120Hz, but you can also try 100Hz and maybe something higher if you like, maybe 150Hz. The correct sounding crossover point can be room dependent, so try a few different frequencies to see what you think soudns best, and to strike a balance you like the sound of.
After all, it's you who has to listen to it....