No, there is non need. Just copy apps folder to sd or usb.
And piibooter.dol and neekbooter.dol? Are they installed on the root of sd/usb?
Once installed into priiloader in either real (priibooter.dol) or emulated (neekbooter.dol) NAND they are not needed at all. It is easier to install them from the root of the SD card so I'd put them there initially.