We've done this before and it worked out well. We had three different people paying their own stuff.
As was mentioned, only one card can be put on the room, but you can still pay with multiple cards. What we did was get a print out of the charges on the last night and took it back to the room with us. We then tallied up each persons charges. At that point, we went to the front desk and paid down the charges separately.
Okay, I hope that made sense.
In short, if total bill is $100 and you charged $40 and sis charged $60, just go to the front desk on your last night and have sis pay $60 on her credit card.
It may seem like an extra step, but it also made it easy to just all use the room charge all week. Plus, we didn't worry about dividing the meal charges until the end. I just saved the receipts and divided them when we went over the final bill.
As was mentioned, the remort will indicate which charges were made with which room card. Also, be sure to do this before the morning of checkout. If you wait until the last morning and have express checkout, then everything will just be charged to the card on account.