Frankly, all three won't hurt. However, I do feel it's a good idea to put your basic requests into your original booking, just to get them logged. Then the next thing is faxing at 3-5 days out, which the room assignment people will at least read individually rather than just seeing your request alongside everyone else's on the computer system.
I don't see any harm in adding requests to your online checkin too -
IF the system allows you to, that is. The old version had no free-format text box so you couldn't do much with it, and I'm not 100% sure how the newly upgraded system will handle it as I can't get it to work for me at the moment. But a fax is better as you can go into more detail.
Venomhatch seems to be this thread's guru of the faxed request and getting feedback. I suspect his PM box must be full to overflowing by now! I don't know exactly what voodoo magic he recommends

but a lot of people praise him very highly for whatever black arts he performs...