I'll answer your last question first. Yes you can turn off internal protection. If you're only going to make minor edits to an existing style, one-touch setting (OTS), or user program group it makes sense to do that.
From what I remember there is a large "button" or "tab" field near the top of the touch screen that allows you to select "Internal" or "External." I would recommend getting hold of a PCMCIA card or PCMCIA memory adapter, and make use of it. If you do a lot of writing or deleting to the internal memory, it could eventually suffer from file fragmentation and slow response.
Also, if you create a UPG that references a user style, and then you move, delete, or rename that style, you may get error messages or unpredictable results. All of this is why with the next generation (BK-series), Roland required all registrations (now called "performances") and user styles to be saved on the USB stick. The E-60 is flexible and more convenient, but tread with caution!
One more thing, I think you can access the contents of the internal memory by connecting a PC to the USB port. Before you start it might be a good idea to COPY and back up whatever is already there. The E-60 is a pretty good board, effectively a baby G-70. Good luck and have fun!!