Denon 3700.4700, 6700 are not optimized to be setup without running Audyssey. If you choose that route it will make it harder to complete the initial setup and it doesn't give you a feel for how the receiver normally sounds or works. Most users follow the manual by going to amp assign and setting up the configuration then running Audyssey. I would suggest this method if you want to hear the unit at it's best. You can always use Direct or Pure mode if you want to turn Audyssey EQ off later. There are so many options but setting up the Denon receiver without an Audyssey run first isn't my first choice.
The Manual Setup discussed on page 228 is primarily for tweaking the Speaker size (Large or Small) / Distances / Levels / Crossovers settings, but if you start without an Audyssey run, Audyssey will be disengaged and you won't be able to try it until you run it. You can
always check the levels with a sound level meter after Audyssey has run,
but it's so much easier to have Audyssey run the initial setup. Otherwise, you start from scratch. I would rather use the tools provided rather than fight the waves.