Bicycle Mechanics - Cross Chaining

I have heard about cross training being an issue with triples, i.e. no small chainring and outer cogs etc. Is it an issue on doubles? I am running an ultegra double and have my chain rubbing on the f.der. in 39x25 and ,53x25-53x19, I am running a 12x25 cassette by the way. Should it be rubbing in these gears? If it is a question of what I ride in mostly, let's just say I don't ride in the big ring too much because it does rub so much. I try to ride in 53x21 or 53x19 but the rubbing surely isn't good for the drivetrain. Should I adjust it? If so, where can I learn how to do that? shedlon brown's website probably? I need to make sure I don't adjust so much that I dump the chain onto the bb right?

You still need to avoid the big-big and small-small combos. The 39x25 rubbing sounds like an adjustment issue with your front der. The 53x25 is definitely cross chaining, but the 53x19 should work if the der is mounted correctly. I have a 12-23 8 speed, and the only combos I can't use are 39x12 and 53x23.

If your derailleur cage rubs in your lowest gear, either the cable is too tight or the low gear limit screw is advanced too far. If the cable is not under tension in this position, try letting out the screw in quarter-turn increments, until the rubbing just stops.

On a 2x9-speed bike, the horizontal spacing between the chainrings exceeds that between adjacent cogs. Therefore, your worst chainlines occur with the two outer cogs and the inner ring and the two inner cogs with the outer ring. Consult a gear chart or run an Excel spreadsheet to determine whether these combinations are, as I suspect, near-redundant with some of your straighter-running combinations.