I know that OTCAS will also accept paper LORs, but I think they just take longer to process. My opinion would be as long as you'll still be in touch with your current supervisor by the time you apply, then wait so they can submit an electronic LOR. That way it will cut down on the amount of time you have to wait before OTCAS says they have "received" the reference (and gives you peace of mind from wondering when they will actually get it).
That's just my personal opinion though, since I did all of mine electroncally and the 3 people I asked to do them said it was very easy. I would imagine that the paper one is very similar though, but then you don't have to ask them to mail them. Good luck!!