Wow...
Ok...So I solved my own problem and once again feel like an idiot. For anybody who is confused as I was, here is what you do if you want to convert your Pandora Battery back to a NORMAL Battery:
1. Do not have any battery in your PSP at all!
2. Make sure the magic memory card is in with the OS Battery Tool that you used to create the Pandora Battery in the first place with. On top of this, if you did not heed the advice and back up your battery's original eeprom to the magic memory stick, then your out of luck (as far as I know) because the application doesn't know what to restore the battery back to.
3. Plug your charger (6v I think) in to the charger slot. Turn Your PSP on and it should boot up like it would normally.
4. Go to the game section and run the OS Battery Tool, and make sure that NO BATTERY IS IN AT THIS POINT.
5. Once the application is running, put in the Pandora Battery.
6. I believe it shows up in green titled as a service battery, and then there are some options that you can scroll through with the D-Pad, one of which says something like convert to normal battery. Hit X on the one that says convert to normal, and there you have it! Your battery is back to normal and you can play your PSP like nothing has changed from the Battery point of Vew.
7. *OPTIONAL* If you no longer have a need for the magic memory stick, go through and format the memory stick, so that it will now be empty if you want the space. You might want to just keep it if you can, and if you can't, try and copy it to your PC so you can save some time if you ever need it again.
I hope this is helpful to whoever needs it (if anybody will ever need it)!
PLEASE CORRECT ANYTHING THAT IS WRONG IF YOU FIND IT!
-Thanks to x3sphere for the guidance, which helped me figure this out.