Wow.
1. Yes, i have an accountant but I'm not overly impressed (for instance, received a penalty notice for late/non filing of corporate tax return yesterday despite it all being in hand with him. I've emailed him and i'll see what he has to say.
If it is anything except "I'm really sorry for the oversight, of course I will deduct the penalty from my next bill" then it's time to say goodbye.
2. When he did my return, he split the drawings i took between personal allowance (put that as salary) and the rest as dividends. But said i must sort out payroll for this year. (my end of yr is 31 March which is why i need to get this sorted)
Every accountant I know would include payroll (for a sole director) as part of the service.
3. Accountant told me payroll can be done online using HMRC tools.
No, you download it onto your (Windows) computer. You can do end of year reporting online.
4. Higher rate tax may be an issue for this year (2013-2014) but not sure how that works if pay salary to personal allowance and then draw remainder as dividends?
Well in that case you will want to have extracted as much profit as possible out of the company in 2012/13 by drawing dividends that (when grossed up) take you to the top of the basic rate band, or that extract all the profit after tax accrued to the end of the tax year if less.
4. Yes, registered company for PAYE as an employer. AND need to operate a payroll to pay myself as sole employee the monthly amount to the personal allowance max for this year to avoid any problems with HMRC.
If you really want to use HMRC PAYE tools the link is here but you'd be better off with one of my other suggestions - or get your accountant to give you a decent service.
5. Not sure what you mean by the Secondary NI Threshold - accountant has never mentioned that to me.
The Secondary Threshold (£7,696 for 2013/14) is how much you can pay yourself without having to pay NI. But my comment about not having to use payroll software up to this point was wrong because you now (as of today) need to comply with Real Time Information which can only be done with payroll software.
6. Nor does he seem to know what i can do about child care vouchers so i still don't know what to do for me to personal benefit from these out of my company!
That's not good, he is costing you £583 a year.
7. Lastly, on the subject of accountants, i was charged about £1200 for the year but that included having the company set up and filing returns. Is that reasonable?
Assuming there are no complications you haven't mentioned you can get a better sercvice than you are receiving (including payroll) for significantly less than £1,000 including VAT.