I have been having some issues with my PC for awhile now, random restarts, as well as a fair amount of what I see as "brownouts." Non-responsive programs happen a lot during the brownouts. I assumed that this was a power supply issue, so I purchased another one. I tried to install it but it didn't work (my old power supply still works in it) Recently when I booted it, it said something about a CMOS battery failure. Could this be causing all of the issues I have been having? I have read that the battery just controls the settings when the PC is off, so I am worried that this isnt the main issue. I am aware that this motherboard sucks, so is that the problem? :(

Not likely. A CMOS battery being completely discharged would likely wind up with a machine that simply wouldn't boot (after losing the HDD geometry). The issues you're having sound more like a possible virus/malware or failing hardware (such as a HDD). The motherboard appears to be fairly recent, so I'd doubt the battery has failed that quickly. Perhaps a better definition of what you call "brownouts" is in order...

Ya.....I was afraid you might say that lol. I hear a clicking sound first, followed by a power down noise....the computer then freezes for 15-20 seconds and then continues again.

The "clicking noise" first (likely the drive trying to access data multiple times before finding it---causing the stalling-out) and then the "powering-down sound" (likely the drive spinning down) is consistent with a failing drive. Backup your data as best as you can ASAP...