I hate setting up guitars :-/

When you guys setup your guitars, do you set the guitar up for the 12th fret harmonic and fretted note to be exactly the same note? Or do you use some sort of temperament?
 
Alright. The guy I know always compares the fretted note on the 12th fret to the harmonic at the same fret and tries to get them identical, so I've been doing the same. Great thread!

Do you compare the sustain of the open string and the sustain of the fretted note on the 12th fret? I'd imagine tuning to the sustain is more accurate when setting up a guitar.
 
I REALLY hate setting up guitars also. My main guitar a Washburn X50 Pro which is basically a super strat with a les paul style fixed bridge with string through body. It is a real bitch to intonate.

The guitar originally came with 9's and I now use 12-52 strings and play in E standard, so I am thinking that could what is causing this mess.

The problem is that I can get all the strings to intonate pretty well except for the low E. When I put the bridge saddle for the sixth string behind where the the fifth string's saddle is, the 12th fret is about 20 cents sharp when the open string is in tune. The only way I can get the sixth string somewhat close is by moving it's saddle all the way as close the the pickup as possible. It definitely doesn't look right, and although the intonation is better than it was it still doesn't feel quite right.

Has anybody had a similar issue that can chime in?