Yes with my towers they're still set to small as my subwoofage is more capable.
80hz is a good starting point, but it's a crossover between speaker and sub, where the low pass filter for the sub and the high pass filter for the speaker "crosses over". Don't know about your subs, but mine are far more capable in the bass regions than even my relatively capable towers. I cross higher than 80 generally, tho.
New speaker break in is mostly about you breaking in, good stuff comes as broken in as you need to worry about. Play something for a few minutes if worried. Not a real big concern no matter what.
LFE would be the cleaner use, as LFE+Main creates more overlap in the lower bass area. More preference in the long run, personally I prefer not to use LFE+Main.
Experiment a bit, in the end its what you like. Many like a little extra bottom end.