Are you sure you only have to check in at the resort and not the port? I was under the impression the only way you have 1 check in, is when actually doing the 3/4 or 4/3 land/sea "package". This may be something I havent heard of yet? We have done the land sea package where we only had to check in once at the resort, and used the same KTTW card. We have also done a stay in WDW followed by a cruise and then we had to check in both times, and use different KTTW cards with each stay.
At any rate, on our land sea package, our rotation was not on our card and we didnt get it until we got to our stateroom. On the trip where we did it separate, the rotation was on our CRUISE KTTW card, however we didnt receive that until checking in at the port.