4 channel amp phasing and gains troubles

[ACDCfn]

Warning, long and complicated stereo phasing/gain adjust question.
Current setup:I installed alpine KTP-445U Amp in my Vaquero, it's a 4-channel amp, 45 watts per channel, that can be set to run at 4 ohms or 2 ohms via dip switches, it has two gain controls, front and rear. I've installed upgraded Alpine DB-521 4 ohm speakers in front and left stock speakers in the Harley tour-pack that say 2 ohms on them. After 3 days of trying I am about to give up attempting to set all speakers in phase and set proper gain levels on amp.
Phasing problem: If I plug speakers according to what my eyes and multimeter indicates (positive wire to positive post of each speaker and negative wire to negative post of each speaker) and then run a test track (http://www.audiocheck.net/audiotests_polaritycheck.php), my ears clearly indicate that speakers are actually out of phase. Even though as far as I can tell visually and according to the multimeter they are plugged in correctly. The caveat is, I am playing phasing test tracks via Bluetooth as the stereo only plays radio or Bluetooth, no cd or aux in. Not sure if that matters that I am not playing test track off a cd but I figure since all of my music comes via Bluetooth so should the test track. So to set all speakers in phase should I be trusting my own ears or the multimeter and my eyes cause I am getting contradictory results from both??!! If I set it according to my ears, multimeter shows that left side speakers (front and back) have a reverse polarity but if I plug them according to multimeter then test tracks sound out of phase.
Amp gain level problem: so I know the formula to set the gains with use of multimeter is square root of watts times ohms. First question, is it ohms of the amp or ohms of the speakers? Second question is, amp can be set to either 4ohms or 2ohms also front speakers are 4 ohms and rear are 2 ohms. Should I be setting it to 2 or 4 ohms? Also since it has two separate gain controls do I cut the result of formula in half and use that number for each gain control?
To top all of it off, all of a sudden I started getting white noise on my rear speakers. Even with gains set to minimal and volume very low still hear white noise. Did I fry the amp? It wasn't doing that before.