Mike, you're now experiencing the horrors of the Denon manual, which Denon has been careful to uphold over the years.
First, as to the crossovers resulting from the Audyssey measurements, the 90Hz and 100Hz settings should be kept. The 40Hz setting for the M22s indicates that in your room location the room gain is sufficient to provide adequate response down to 40Hz. This doesn't mean, however that it should be left there, since a good sub should be given more room to handle what it does best, up to say 80Hz.
The 1712 has a range of crossover settings from 40Hz to 250Hz available(see manual as Randy suggested, especially p.62). To set the M22 crossover to 80Hz, you use the "Advanced" crossover setting(yes, the regular manual crossover setting is global). To get to Advanced the 1712 may use an extra enter click or you simply try to go above 250Hz and it then switches to Adv(of course, the manual doesn't explain). The other settings shouldn't be changed; the data stored from the Audyssey measurements remains unchanged, and only the manual change to the M22s has an effect despite the Audyssey data.
The sub setting should remain at "LFE", not "+ main". That + setting would require the M22s to be set "Large" and run full-range, not a good idea.
No, the Dynamic EQ has nothing to do with the setting difficulties. It should be used at all times, with the only caution being that if some unusually loud popcrap CDs are played, the bass emphasis at lower than 0 volume settings may be overdone and result in some boominess(the compensation is designed for "average" loudness material). For such extra-loud stuff there's an adjustable Dynamic EQ offset which lessens the bass boost for them.
