We have had two a very long time. Some points:
If currently purchasing both contracts, make sure that the two contracts are deeded to the same names and that Disney is informed by closing, through the broker or otherwise, that the same persons are purchasing the contracts and that you want both to show up in the same online account. Those are the initial steps needed to assure nothing gets screwed up and you end up with both contracts in the same online accounts.
For all essential purposes, the two memberships will be treated as if you were two different members. Each use year has its own banking date. You will receive separate annual budgets and annual dues statements and if you have automatic monthly withdrawal for your dues from your checking account, there will be two separate monthly withdrawals. The points in the two use years cannot be mixed to reserve any single night and thus if you want to use both use years for a single trip, you have to either transfer points from one use year to the other and then do the reservation, or instead book part of the trip with one use year, the other part with the other use year, and then contact MS and have the reservations linked so you will avoid having to change rooms. And note that if you do that transfer of points you will not be able to reserve online with any transfered points and instead will need to call MS, thus giving up the one hour online advantage if you are tryng to book something that can disappear quickly at the 11 or 7 month window. If instead you do the two separate reservations and then link, you have the different issue that each reservation will have its own arrival date for determining when you can reserve at 11 or 7 months out.
Each membership will be entitled to have two active wait lists at any given time, and you can purchase one time use points for each membership, meaning you can actually get up to 48 one time use points for a single trip when you are using both use years for one trip However, that only works if you follow the method of making two separate reservations rather than using a transfer of points for the trip, and do the one time use point purchases before attempting to link the reservations because once linked the reservations cannot be modified without MS first unlinking them.
Each membership gets to make one transfer of points per use year and thus you effectively have a two transfer per year right. Also, MS will usually let you do multiple transfers per year if they are done only between your two use years. If you go two times a year, and use only one use year per trip, you can avoid the risk of losing points due to a cancellation. You have until the end of the eighth month of the use year to bank points. If you schedule a trip to occur late in your use year and have to cancel, you face the risk of not being to bank the points if you are beyond the eighth month of your use year when you cancel. With two separate use years like March and September, you can use the September use year for a trip in February or March and the March use year for a trip in July or August and avoid that cancellation/inability-to-bank risk.
Overall, we have not had any real problems with two use years and it is not any huge additonal burden just to have to deal with two rather than one use year.