Yes. The only reason you would not have any carryover funds is if your stake has you cut them a check for your remaining 2011 balance. Once they give you the funds, they are yours and yours alone. Your 2011 ending balance is now a carry-forward balance for 2012, whether it is negative or positve. Incidentally, CHQ never took the funds back; the stake did. If it helps, I think of it as before the entire stake shared a single account and the stake told you how much of the total you could spend. If you went over, you hurt the other wards, if you went under, it remained in the account for the stake to use for budgeting the next year. Now each unit has its own account. If you go over, that's yours to recover from but if you go under, the surplus is yours to use.
At the end of the quarter, the only thing that happens is you get the funds for the next quarter. Nothing happens to your funds. You should be budgeting based on a yearly estimate, but the funds are disbursed to you in quarterly increments. Incidentally, this is how it has always been done, but most stakes did the yearly estimating for you. Now it is the ward's responsibility.