...i have no clue how to actually clean a bugged file, and from what i can tell so far from the scans, i have alot
Once the scan completes, with either Malwarebytes or Superantispyware, you click either "Next" or "OK" and either program will go through the removal/cleanup process automatically. You will most likely have to do a reboot after each scan if there are files to process. If you were in Safe Mode, make sure you boot up again in Safe Mode to run the next scan. I highly suggest that you run the scan's multiple times.
If the same bugs keep showing up on subsequent scans, you have two options:
1) Remove the drive from this machine, mount it on another and run the same scans there. This is most likely the simpler route, if you have a spare machine available, rather than making a live boot CD to scan from (also recommended if you want to make one though).
2) Format and re-install the OS. This way you are guaranteed to have all the bugs removed - unless you have a BIOS infection...but those are quite rare.
Once the computer is coming up clean, I suggest grabbing
CCleaner and
Defraggler to clean out unecessary files and registry entries and to defragment your hard drive. Both of those tools are more efficient and somewhat more effective than the built-in Windows variants.