I'll chime in with what I can help out with here. I can't really say I use the Inno-Sport system exactly to the "T", but I do try to incorporate a lot of their methods, especially fatigue managment.
1.) Deadgame pretty much hit this on the head as far as I see it. You should generally have an idea of what your "best performance" for the day is, and then drop-off from there. Also, don't overuse pinnacle work, I made that mistake and my progress was frustrating. Now I use prime drop-offs and I find it's much easier to apply. Pinnacle is good for fatigue cycles though. Testing your "best performance" works better for the AN-2 bracket, IMO. If you are trying to do AN-1 work, and you work up to a true 1RM, you often won't be able to drop the weight 6% and hit another rep- at least I usually can't. However, say you are doing bench in the AN-2 lower bound bracket, you might want to pick a weight that you know will be failure from 6-9 reps, then just rep that til failure. You'll usually be able to drop the weight (or reps) 6% (or whatever your desired fatigue is) and hit it for a few more cycles.
2.) It depends where I'm at. Usually, I too can't do a few circuit. A lot of times I can if I'm doing lower body, I can just get in there and hog the power rack, but I usually wind up splitting into 2 circuits. What I do is split up into "important" and "less important" circuits. The important circuit is no more than 2 lifts and the less important is no more than 3 usually, maybe 4 if I'm in a higher bracket. The "important" circuit gets more fatigue than the "less important" circuit.
Here's what I mean:
Upper Body, DUR An-1/An-2
"Important" ~5% fatigue
A. PIM Bench, N x 1 rep
B. ISO Bench, N x 5-9 seconds
"Less Important" ~2% fatigue
A. PIM Dumbell Bench, N x 6-8 reps
B. OI Triceps, N x 15-20 seconds
C. ISO Pull-Up, N x 15-20 seconds
Basically there is no drop-off on the "less important" circuit. If I get 8 reps on the first set of dumbell bench, and I have to really really strain on the 8th rep, I'll only do one set. If I feel like I can get another set or two of 8, then I will. Remember that the supplemental stuff is just gravy, especially for athletes.
3.) I'm lucky enough that both of the gyms I train at have a clocks that are visible from pretty much every machine. As squattin said, don't worry so much about the time, have a buddy time a couple of warm-up sets of a few different exercises and you'll pretty much be able to know what brackets you're working in for just about any combination of exercise and reps.
As an overall, I still feel like I'm generally basing my training off the WS4SB template, only I've tweaked it in terms of exercise selection for my sport (volleyball), and I try to use the Inno-Sport principles to guide fatigue management. Remember that the goal for athletics is always to raise your "MAG" proficiency or magnitude of force manipulation, you do that by:
1.) Training your CNS to send a more powerful signal, through max-strength and MAG work.
2.) Being able to output a signal more quickly, with rate work.
3.) Being able to hold onto the tension longer, with dur work.
It's generally not that complicated, if you're weak, do DUR+MAG, if you're slow, do RATE+MAG.
Alright, that was pretty rambling. Feel free to ask me questions and I'll try to clarify whatever I can.