I actually own the DVE disc so I'm not that familiar with the AVIA disc. Looking at the table of contents for the AVIA disc online, it looks like it gives you a whole slew of options for subwoofer tests. I would honestly try them all. Just make sure you're doing them while at reference level and sitting in your sweet spot. By ear, you're trying to find the most seamless transition from speaker to speaker while performing any of the sweep tests. You can back up your ears by watching a SPL meter while doing the tests as well. Oh, and forget the acoustic bass or piano tests. I made a mistake and missed where your crossover settings are. They're way too low for you to notice any difference with a 40hz setting.

My instinct would tell me that your second setting choice of "Large and LFE for sub" would be better. Why? Well, you got the "L&R" covered with your towers. Again, you gotta trust your ears to make the final judgement.