I always use an O-Scope to set gains. It is the most accurate way of setting gains to ensure a clean, unclipped, signal throughout the entire path.
Set all EQ's, crossovers, boosts, ect to "0" (or off) to ensure nothing is messing with the signal.
Use clean sine waves between -3 and 0db at 40hz, 400hz, 1khz, 4khz, and maybe 10khz (I generate mine at 0.8 on the linear scale, which is about -2db and I typically throw in 25, 60 and 100hz as well for good measure, but that's a tad overkill). I use waves or flacs, but even with mp3s, on sine waves, there is no difference.
Place O-Scope on the RCA outputs from the head unit, I typically use the 1Khz on the front and rear channels and 40hz on the sub channels. Turn the head unit up until the signal starts to clip, the back it down to the maximum unclipped volume. This is the maximum you can turn up the head unit before introducing a clipped signal to the processors or amps.
Do the same for the next piece of equipment in line (some processors have an input and output gain. If yours doesn't, make sure the signal comping out of the processor is unclipped at this volume on the head unit).
Finally move to the amps. For sub channels use the 40hz, for mid-bass channels use the 400hz, for midrange use 1khz, and for tweeter channels use 4khz (or 10khz). If it's just F/R/S, the 1khz on F/R channels should be sufficient. Place the O-Scope on the speaker outputs and adjust amplifier gain until the signal starts to clip, then back it off till the signal is pretty again.
Now your done with the "amplifier tuning".
In between here and the next part I will use a microphone, laptop, RTA, and pink noise to make tuning adjustments to the primary DSP (PEQ curves, time alignment, and crossover points). If you don't have that, don't desire it, or just don't want to, then move on to the next part.
Now set your crossovers, EQs, boosts, etc. to whatever meets your preferences (and equipment). Just remember if you use a lot of boosts, you should be careful turning the radio up to the maximum point discovered in the first step, as you could be clipping the signal. Clipping sounds bad, and if you do it enough, it can damage the speakers. The only subs I have ever blown (me, not a faulty piece of equipment) was like 33 years ago and was due to me clipping the hell out of them. Luckily, Cerwin-Vega was a different company back then than they are now, and they re-coned them for me for free, even though they were more than a year out of warranty. However, I learned my lesson, and haven't done that since. With music, during a heavy jam session, some of it is going to clip, and you may not even hear it. What you don't want, however, is to be playing "Bassgasm" at full tilt, constantly clipping. That will likely fry your subs and is why you want to tune gains with an O-Scope at the head unit, all amps and all processors.
This is my opinion, based on 34 years of car audio experience. This is not the "only" way, but it is, in my opinion, the "best" way.