LFE vs LFE+Main is more a preference thing. Personally I prefer to use LFE and start with a crossover of 80hz, but usually cross higher. The LFE+Main mode will double up the bass somewhat as there will be an overlap.
How is zone 2 delay an issue? I don't think there's any way to adjust it, tho.
Amp assign on page 39 of the manual....which speaker format matches your setup?