I would suggest using UPS since FedEx has a tendancy to loose or be late with my packages and they have been known to not be able to find my house although UPS has no such problems. I suppose they would let you use the original box but they would probably require you to by another box to put your original in. This would in turn make your shipping cost even more. I would just take the PS3 to a shipping location and have them select a box and package it in front of you for you.
Call sony and tell them your problem and they will troubleshoot your system. If you are in warranty you will have to have your receipt if not you can pay. They will send you a box for your system threw Fedex. Inside will be a checklist on what you need to do. This checklist will involve deleting everything on the device (THIS TAKES ABOUT 6 or more hours). There will be a card in there to fill out all your information including the problem. After that you take your system to a FedEx location and drop it off.They will give you a receipt so you can track your system!.!.! HOPE YOU FIND THIS USEFUL!!! Oh yeah make sure you eject the disk and send no cords with the PS3!!!
I put it in the orginal box its pretty sturdy with those cartons it fits on the side but you could put some bubble wrap around the ps3 it self to be safer. as long as its tight it will be fine. make sure its marked fragile though