Home or pro makes no difference . . . the devices are designed for upstream volume control - either from an FOH mixer in live, or whatever preamp is upstream in home use. To that end, about the only diff home to live is who is in front of the system. Set input gain so that input level is just shy of peaking sending the *hottest* signal you anticipate sending, and match output levels and amp input gain to give the corresponding level in the room. The goal being to use the largest about of the resolution of the A to D in the unit, without overdriving it going in, and setting output levels on the back end to be well above the noise floor of the output and the amp preamps. Ultimately, if you already have a gain structure in place, this will likely result in settings that result in the Drive Rack looking like nothing more than frequency selective wire. Can't say that I am famlliar with your sub setup, but myself, I would cross the subs on the Driverack as well to ensure that appropriately matched crossover profiles are applied to the sub vs mid crossover, and insert any other sub processing you may still desire between the DriveRack and the associated sub amp. (Also note that a separate sub crossover than the D/R prevents you from using the subharmonic synth in the D/R, should you have an interest.) Remember: this is a DSP crossover, and *NOT* a preamp, and treat it accordingly, and you should be fine. You don't control volume in an analog crossover, and this really isn't any different.
On eq, on pro stuff, the PEQ is tyoically done to address bumps in the native response of the system (typically provided by the system mfg) and the GEQ is used for rom tuning, but it isn't a hard rule, or exclusively. Myself, in all cases, I tend tomuse PEQ to take out bumps in the device response, and GEQ for the system to eq flat in the near field. (Don't want that argument here . . . out of context). With the system tuned to flat, I then do room/taste/etc. tuning upstream. (This is more in the live case where spaces change - you can put your specific room setup in the GEQ as well, if desired).
Oh, and while there is no "right" way, If reasonably close, I tend to set all amps to the same level, and make specific balance changes in the D/R outputs. Amps are more likely to get accidentally changed than a DSP setting, and are easier to "put back" if all are the same.
If you have kids (or others) prone to abusing the system, set all amps at full up, match the D/R to give the correct max output, and set limiters in the D/R capping the output at a safe level. This way, if itchy fingers want to turn it ip, they will find no more control range to do so (I do this at my church on the systems in youth areas . . . beats the heck out of changing diaphragms/drivers in the air!!!)
Oh, and I have really never found use for the auto eq in the Driverack due to it's limitations. Myself, I use SMAART and can do a lot more - phase and time alignment, multiple sample points . . . It also can send it's own test signals (impule for time alignment), and loops it's reference channel back via the interface in use, thus removing any artifacts due to the interface, and can also give you a transfer function of the system running live program. (REW does a lot of this without the price tag, just had a SMASRT license first . . ). Tuned up some very high end floor monitors with SMAART and a DriveRack, and it was amazing how much time alignment cleaned up the crossover points.