The thing I don't understand is that you supposedly can't ever correct valleys by bumping up frequencies. If that's the case, why do EQs even have the ability to increase FR, instead of just making cuts?
Step one is to try to adjust using the tone controls. That can help bunches with a simple solution to a relatively decent room.
Next step is the typical graphic sliders most folk try, Yes, those are a bit more flexible than the standard tone controls, but those are the next best thing to useless for accurate tuning except for BIG lumps in the spectrum which should be taken care of with room treatments anyway. A big problem with those is adjusting one slider also affects those around it ... and yes, it leaves those bumps and valleys you mentioned. The more bands available, the more you can minimize that sort of thing, but the problem frequencies can cover an extremely narrow band inside the wide band covered by the slider control and kill a lot of good stuff too.
Next step up the ladder is an analog parametric equalizer that you use to dial in a problem frequency accurately, as a parametric allows you to adjust both the exact center frequency AND exact bandwidth you want to adjust. Those can drive you crazy, as it's difficult to know exactly what the problem frequencies are. Solution there is to test the room using software that can "sweep" the spectrum and show you the actual results in the listening area. There again, the problem is the hard limit on the frequencies you can adjust based on the amount of band controls available on the PEQ.
Ultimate solution is a digital software approach. Do the same frequency sweeps you'd do to test a room when setting up any of the other EQ/PEQ solutions mentioned. Difference is, the frequencies you can adjust are limitless, and you can really dial in a room for perfect response across the spectrum. Here's an example of the level of detail you can get, which runs rings around any other approach ...
(Target frequency, +/- decibels)
10 -4
12.5 -3.5
16 -3
20 -2.5
25 -2
31.5 -1.5
40 -1
41.172 -0.9475
42.379 -0.874
43.62 -0.8015
44.9 -0.75
46.214 -0.6565
47.568 -0.6565
48.962 -0.584
50 -0.5
51.874 -0.435
53.394 -0.361
54.958 -0.2555
56.57 -0.25
58.226 -0.1055
59.932 -0.0585
61.688 -0.0205
Etc, etc, etc, all the way to the top.
I use a hybrid approach here. All my library is now digital, but I still like to spin an SACD or vinyl regularly. The digital software handles all the digital sources, and I use a PEQ for the SACD player and tables. I use the same frequency sweeps used for the software to set up the PEQ, but have to pick and choose the major excursions due to the limited number of controls available on the PEQ.
Still runs rings around what I hear without it.
And just to prove how anal retentive I can be about the whole thing, here's a form I made for setting up the PEQ ...
... and yah ... I know ... I've gone to the dark side. I really need to seek professional help here ... <G>