I am a provisional tax payer, but I want to claim on my annuities at year end, where do I do that?

You will only be able to claim any annuity payments on your year end tax return. However you can show the income less this amount on your "taxable income" block on your IRP6 which will reduce your tax paid in this period.

If I fill in a ITR12 at year end but also did my second IRP6 and paid according to that, wont SARS also charge me on the ITR12? for the same income?

SARS only charges once for income earned through the year. The IRP6 is just a way of SARS getting cash earlier and helps you from having to pay a huge amount at year end. Whatever tax is paid during the provisional period, reduces your year end liability. So you can see it as paying up front for the income you expect to earn during the year, but never twice!