There are two elements that you are confusing yourself with here I think.
1. Yearly ISA allowance
2. Maturity of your 12 month Cash ISA investment.
Let's deal with each one separately:
1. Your ISA allowance for the 2011/2012 tax year is £10,680 . However, only half of this (£5,340) can be paid into a Cash ISA. The remainding £5,340 must be paid into a stocks and shares ISA, or just left unused. You get an ISA allowance each tax year and the ISA allowance for the 2012/13 tax year will be £11,280 (half of which can be paid into a cash ISA).
2. It sounds like you have taken out a 12 month fixed rate deal. If you do nothing the account will continue and you will revert to the bank/building society's standard rate (which is usually much lower than the offer rate which they advertise to hook you in). You can simply transfer the account to another bank who are offering a better deal. Once the money is in the ISA you can switch it around from bank to bank and this does not count against your allowance as it is already in an ISA.
You can take out as much as you want, whenever you want. However, if you 'tie-in' the cash buy getting a 12 month fixed rate deal then encash after 6 months say, the bank will deduct a significant amount of interest from you as you have not kept the money with them as agreed at the beginning of the term. If you wait until the deal matures you will get the full amount of interest (tax-free) and then can take out whatever you want without penalty.
I hope this helps?