The effects of the room totally swamp anything that the electronics might do, so you'll be just fine trying to quantify the effects of your room with a separate amplifier.
If you want to do this systematically, I would start by stripping down all the acoustic panels and then find the best speaker and listening positions...once you figure it out, you should start by looking at the ETC and get an idea of how the sound is bouncing around the room. Although there are some levels where this is just intuitive, it is going to depend highly on the power response of your speakers. The polar response at any frequency is going to be different which means different reflections are going to contain different frequency content. Generally speaking, you're going to see wider polars at the lower passband of each driver and narrowed polars at the higher pass band of each driver. For instance, a 12" woofer is gonna start beaming at 500Hz and be really obvious by 1kHz, while a 4" mid is going to be really wide at 1kHz and start beaming around 3kHz (and be really obvious by 6kHz).
Anyways, since you're probably not going to get accurate polar data from your speaker manufacturer and really you're only interested in the real reflections (not predicted ones), you can directly see what is happening by looking at the ETC. After that, it's pretty "simple"...you want to find ways to remove early reflections, but you also want to find ways to add more late arriving reflections so that you end up with a dense reverberant field instead of a few sporadic specular reflections. Early arriving reflections would be defined as reflections happening inside the Haas window, which is a minimum amount of time that needs to pass in order for two sounds to be heard as two separate and distinct sounds. Two sounds that happen within the Haas window are perceived as a single mushed up sound. In this case, you have the direct sound of the speaker (traveling the shortest path to your ears) and then you have the reflections (traveling a longer distance and thus arriving later).
If you just absorb the early reflections, then you have no more energy to bring back after the Haas window. This is why most acoustical treatment regiments involve a lot of diffusion and diffraction instead of absorption. In a small room you'll be limited by what you can accomplish, in which case you want to make sure that once the first reflection happens, that you try to maintain a dense and linearly decaying reverberant field. The next most important thing here will be to make sure that you don't have any strong late arriving reflections (which will show up as spikes rising higher than the reverberant field).
Btw, I probably should have mentioned it earlier, but you'll want to treat the bass first (bass traps, helmholtz resonators and all that shnazz)...the biggest reason is because they're harder to treat and will "inadvertantly" affect the MF/HF as well...it wouldn't hurt to think about the possible advantages to the MF/HF while you're treating the LF.
Anyways, as you add panels (do one at a time), you should see changes in the ETC. If you don't, then the location of your panel isn't doing anything, which means you've probably got the panel in the wrong location. The important thing here is being able to keep track of which reflections are because the mic is close to your listening position, or because the speakers are close to a wall ("early reflections" will show up in both places).
Btw, since it sounds like you've already got a bunch of treatment, you might just start by measuring the room in its current state and see how close to the ideal you are.
Page 2 in this pdf has a great picture of the ETC's before and after treatment:
http://www.rpginc.com/cgi-bin/bytese...ary/HT_AcD.pdf
It also labels and describes some of the terms I'm using too.