Running both fans from one sides power source will just kill the other one before long.
Messing around the fan connector has nothing to do with drive flashing, so it's hard to tell what the exact problem is if you've been poking around back there. In most cases like this it's just a shot Transistor, QA32 (top) or Q3M1 (bottom) and replacing it will solve the problem, but it's easier to just get the voltage to power them from somewhere else.
Doing that ya loose the thermal control the fans have, they can range from 5v to 12v depending how hot the 360 is, and if ya don't like the 12v idea run them at 7v or 8.7v which are a good balance of airflow and noise. You can use a SPDT switch and run them at 5v or 12v so you can change them whenever and there are more than a few fan mod tutorials and such in the 360 Case/Hardware section to go by or get ideas from.
The 4 pin fan connector has 2 grounds and 2 power, the power pins are independent of each other, the grounds are connected together on the board. Red/Brown are the + and Black/Blue the - for the fans.
Switching grounds wouldn't do anything, they're the same.
Since ya know what color wire is what now it's more than easy enough to figure out what pin does what on the fan connector, and here's a schematic if ya want to get any further into it.
http://forums.xbox-s...&...t&p=4035646