Dr. P (great name, btw),
Welcome to the forum. Here are some general answers to your questions. I also suggest that you peruse the forum here, as well as checking out the "Tips & Tricks" menu at the top of the main Audioholics website site (there are articles on speaker calibration and set-up). IMO, the answer to the following questions is to experiment and use settings that you prefer. However, the answers below are general guidelines.
1. Should the speakers listed above be set to large or small?
Typically, you would set them to small. If the speakers aren't as capable at bass as the sub (and most aren't), then you'd set them to small.
2. Depending on the answer to 1, should i output the low frequencies to both the fronts and the sub? or just the sub?
If you set them to small, then just the sub.
3. What should the crossover be set at on the sub? Should this setting match on the receiver menu?
If you set the crossover frequency on the receiver (80 Hz is the THX recommendation), then you don't want the subwoofer to also try to apply a crossover. You would set the crossover frequency on the sub itself to the highest possible setting and/or disable the crossover on the sub (some subs have an input that bypasses the crossover, some subs have a toggle switch to disable the crossover, and some subs don't have either).
4. How do i know whether to set the phase switch on the sub to 0 or 180 ? should this setting match in the receiver menu?
Here's where my knowledge breaks down. I believe that you just need to try both and find out which one works the best in your room with your placement of the sub. You want to use the setting that provides the best response.
Again, just general recommendations. Try out some settings and see what you like. I'd appreciate it if you'd let us know what you end up using. Thanks!
Adam