Front Derailleur Adjustments

Are you adjusting it with the two set screws or are you adjusting it by rotating the entire derrailleur??

The two set screws allow you to dial both the upper and lower ranges independently.  If you are in your 39 x 23 (assuming a 53/39 with an 11-23 cassette) then you should not be rubbing on the inside part of the der.  When you shift it down to the other extreme of the 39 x 11, then you will get some rubbing (because of the cross-over that you shouldn;t be doing anyways).

After checking the low, you go to the 53 x 11 to check the high, and same thing, adjust it so that there is no rub.  Then go to the big chainring extreme in the 53 x 23 and you'll probably have some rubbing.

If you are getting rubbing at other times then the der. is probably not aligned with the chainrings correctly in the first place and the set screws won't help as much.

For actual shifting, I strictly go by cadence.  If I'm doing 105+ then I shift up.  If I'm going downhill or have a tailwind then I'll just go ahead and get in the big ring ahead of time.

I personally never use th 39 x 12 or 11 (I have an 11-23 for training, 11-21 for racing) or the 53 x 21 or 23.  Those are just too extreme of a cross-over for me.  So I effectively only have 16 speeds, of which about half are overlapped gearing depending on if I'm in the big or small ring.

On a rolling terrain I'm constantly shifting to give you an idea of my approach.  There is no specific time in the gear sequence you should shift to the big really.  It is whatever works best for your pedaling style and cadence.