It can be done, but you must keep careful records and always make sure MS is using the points you intend when you make your reservations.
The points will all retain their original resort and use year for banking and borrowing purposes. So treat them totally separately this way. Also remember they have their own 11-month/7-month windows. Banking, borrowing or transferring doesn't change these windows (except you can actually lose time on some points if you transfer....see the thread on that one that's also here in the
DVC board)
You can make reservations using both accounts, but you can't combine the points to do it. For example you need 100 points for a 5-day stay. You can't use 50 points from each account to make the reservation. You can however use 60 points from one account to reserve 3 days, and 40 points from the other to reserve 2 days, then link the reservations.
The other option above of course is you CAN transfer 50 points from one account into the other, then use the 100 points total to make the full 5-day reservation.
For your example, let's say resort #1 is a March UY, and resort #2 is an August use year. You want to make a ressie for May,2003.
May 2003 is in your resort #1's 2003 UY, but is in your resort #2's 2002 use year. You make the ressie as explained above. Just keep track of the points. Some came out of a 2002 use year while others came out of a 2003 use year. Essentially you made a 3-day reservation with one set of points, and a 2-day with the other set. Treat each one as if that was the only ressie you were making. They are totally independent of each other, and only the final 5-day stay is continuous because of the linked ressies.
Transferring the points makes it possible to use points that otherwise could not be used (EG 50 points is enough for 2-days but not 3 days @ 20 pts/day). But even after transferred they still retain resort and UY identities. Keep in mind, I don't think you can transfer banked or borrowed points.
Bottom line, is it a pain in the butt? Well, it CAN be, but it all depends on you. In our case our contracts are only 2-months apart (June and August) so it's not so bad, especially since we travel mostly in the Sep thru May timeframe.
Good luck.