Kinda muddled question here. Chain line issues are more related to SS IGH bikes. Derailer bikes rely on unclean chainlines to work.
The basics is that the bike as a mechanical thing will perform best when the chain runs as straight as possible, and that you as a biological engine runs best at a certain cadence.
Somewhere between these two is the golden compromise, where neither you or the bike is hurting very much.
Running on the small chainwheel and the smallest sprocket or the biggest chainwheel and the biggest sprocket is called cross chaining and is generally frowned upon, particularly if you're running a triple front.
Exactly where cross chaining is beginning to hurt is an open question, some will avoid only the last sprocket at either end of the cassette, some will avoid the two last sprockets at either end of the cassette. Some will say that using all sprockets from the middle of a tripple is OK, other will recommend avoiding the last sprockets at either end even from that position, and so on.
As (hard) cross chaining usually is pontless in terms of the gearing it gives(which usually can be had at other, mechanically less stressful combinations of chainwheel/sprocket as well), there's no need to go there anyhow.
So:
1) avoid the extremes which aren't doing anything for you anyhow.
2) pick a cadence that keeps your heart and knees happy.
3) then spend a little effort on which combo which'll give the straightest chainline for that cadence.