Hi Fred,
You can see how the gain structure works by looking at the schematics of the preamp units, but here's a quick primer. I'm going to mention N72s and J99s, because those are what I own and have experience with.
The trim control is an attenuator; on most of the SCA preamp circuits, its range is -6 to 0 dB. In the case of, say, the J99, you'd use the trim control for minute adjustments to the input gain, since the gain switch sets the gain in 5 dB steps. I always run the trim control fully-clockwise to start. It's important to note that this isn't "turned all the way up"; rather, that's the position where it does not affect the signal. If, during a tracking session, I see red lights on any of my tracks, I will slowly and gently turn the trim control down a little bit. A 5 dB drop would absolutely be heard, but a gradual trim down would not. Unless you have a reason to do otherwise, run your trim full-open. I will present a reason to do otherwise in a moment.
The gain control sets the signal level that the head of the gain stage receives. It is not actually a "color" control, though the way you adjust it can affect the overall color of the pre -- more about that in a moment. When you set your gain, start with the gain fully counter-clockwise, and your trim fully clockwise. Have the musician play the instrument while you watch the meters in your DAW or your A/D converter. Turn the gain control up until you're getting the signal level you want on your meters, using the trim to adjust if necessary.
Now, the N72 is a little different from the others. The trim control is in between two gain stages, and can be wired as a full fader (the 0-100% you were referring to). I set my N72s up this way because it opens up more tonal possibilities. With the N72, when you hit the first stage really hard and pad it down with the trim control to keep your A/D from clipping, you get a sort of gentle compression effect. (You're really unlikely to ever actually clip the N72 -- it has enormous headroom!) If you just run with your trim control fully clockwise, and set your gain appropriately, you will get the cleanest sound from the N72. But you can really abuse the N72 by using the trim to pad down its output, and boosting the gain a lot. This is a tonal possibility not so much because the gain control adds color, but because you've hit the input so hard that it's starting to overload, and the output would otherwise be ridiculously hot, driving your A/D well beyond clipping.
For snare and kick, I use my N72s exclusively; those are the loudest sources I take in, and the J99s with gain and trim at minimum can
still clip the A/D. So, with the full fader of the N72, I get extra trim range to prevent clipping. (I could also put a pad in-line between the mic and pre, but why would anyone want to do that, when they can drive the pre hard and get that tasty mojo??)
Your link to the A/D manual didn't work, but usually an A/D's input sensitivity can be set to, at minimum, +4 dBu or -10 dBv. When using your SCA preamps, set your input sensitivity to +4 dBu. When you stage your various gains, you want the signal as hot as possible as early as possible. For example, if you can get away with turning the pad off on your mic, do it. If you can turn your preamp up higher without clipping your A/D, do it. The logic here is that every amplifier and buffer the signal passes through adds a bit of noise. The more gain that is required at each stage, the more the cumulative noise from upstream is going to be amplified.
