1. Only your basic pay really matters for the visa, so as long as each payslip is at least £1,550 before tax, you meet Category A. The overtime will be counted when they calculate how much you have been earning for the last 6 months, but only your base salary will be considered for your future income and employer letter.
2. Your total annual salary is your base pay, as stated on your contract and your employer letter. If your base pay is £3,000/month, then I assume your contracted annual salary is £36,000... so that's what should be in your employer letter and on your application form (the overtime is an added extra, but won't be included when they work out your future annual salary).
3. You are category A, so you provide 6 months of payslips and bank statements (well, 7 months to be safe). You would only use Category B and 12 months if you earned LESS THAN £1,550 in any of the last 6 months. There is no reason for you to even consider Category B, because you do not have a variable salary - you earn £3000 base pay every single month.
An example of when you might use Category B is if you are not on a fixed annual salary and maybe you only work some months and don't work other months, or you earn less than £1550 in some months and more in other months.
For example:
May earnings = £3000
June earnings = £1500
July earnings = £4000
August earnings = £0
September earnings = £3000
October earnings = £1000