It is important that you present a Visa card at checkin. I used an Amex at checkin a month or so ago but paid with a Visa. Had to call MR and get it straigthened out.

This is what I do...

Make rez with Amex on file on web site.
Present Visa at check in.
At checkout, ask to have room charges paid by Amex. Other stuff like room service, I leave on Visa or present Visa debit card to pay for those. You could even tell them to put $20 on a Visa and leave the rest on Amex.