I think you've got it figured out.
Keep in mind Arena was built for computer v computer matches... the no background progs running etc. also keeps things fair for your engine matches and just generally reflects the mindset of someone who's got his computer running engine v engine matches.
By the way the latest stockfish, and Fire 1.2 are very strong free engines... Fire in particular is screamingly fast and strong. I recommend both, and Fire 1.2 if you can only afford one free download ;)
I don't know much about using chess engines aside from the very basics. I also don't care about the latest and greatest-- the freebies like Rybka 2.2, Spike 1.2, Pro Deo 1.5. etc. are fine for my purposes. But I'm a little confused as to the best method to analyze a game.
I've got Arena 2.0.1, and most of the advice I've seen is to set the analysis for a certain time per move, rather than a particular ply depth. Then they go on to point out that for maximum analysis power, your CPU shouldn't be doing anything else during the period of the analysis, so one should have this running while no other programs are being used, and should even disable screen savers and blankers, anti-virus programs, etc. so as many CPU cycles as possible are devoted to the chess engine during its time period for each move.
Well, that makes sense, but bottom line, it ain't gonna happen. My analyses are going to be chugging along in the background while I'm doing other things on the computer at the same time, and I'm not going to bother disabling all of my normal background utilities every time I want an analysis. So I understand the analysis output will suffer if I'm using the minimum time interval setting. But what if I instead use a minimum ply setting, like 15 ply or whatever-- is the amount of other simultaneous CPU work going to reduce the quality of the analysis aside from increasing how long it takes the engine to get through the 15 plies? If I'm occupied doing other stuff, I don't care that I'm increasing the analysis time. But would I also still somehow be reducing the analysis output quality even with a minimum ply setting instead of a time setting?
Lastly, what's a reasonable minimum ply number? The Help file suggests that 9 plies will almost always result in the best move. I've run through a couple full games set at 15 ply depth and am perfectly happy with the amount of time that takes in the background for a 25 to 35 move game while I'm doing other computing.
--Cystem