If memory serves, there are independent channel calibrations for DD/DTS and the multi channel input so you need to calibrate for both scenarios.
If you set the processor for 5.1 and don't use a sub, the LFE channel will NOT combined back to the mains. You need to go into your DVD player, turn off the sub and make sure you have your processor set for no sub as well and the mains large. I strongly recommend getting a sub however.