I had heard that they don't see it until about 3-4 days out (or at least start doing anything with them until then). Personally I think it's better to fax, because then they'll attach it to your reservation. If you call, depending on how motivated the CM is, and if they grab another call right after yours, etc., they may say they'll make the note, but not actually do it. Think if you're really concerned, I'd fax it over around 4 days prior, and then maybe call the next day to see if they received it and have your chart noted properly.
All we really want is top floor, so I have that noted already and I'm hoping a fax 4 days beforehand should be enough. If not, even though I checked in online, I'll wait in the regular line if I have to in order to get it changed. But I can't imagine it should be a huge problem! Good luck and say hi if you see anyone with a DIS shirt on!