When comes to VAT quarter the accountants will work out the VAT flat rate of 11% and send me this amount to my bank account so that I can pay to HMRC. I clearly don't understand . Should the VAT and Net payment normally paid into my business account and when they calculate the VAT 11% they should let me know the 11% amount figure and I pay to HMRC from my business account?
Are you sure this is what they said, did they not say we will set up direct debit of your behalf and submit vat returns - we will then tell you what funds will automatically be collected from your bank account?
If it's as you say this may work for their clients but it's a pretty nonsensical arrangement unless someone isn't able to do the basics of running their own business, you ask the obvious question as to how they have the funds to pay in the first place to be able to pay you the vat. You issue invoices direct to your client and they pay you - any other arrangement means you don't have control or access to your money without hoping that it will arrive when you ask them for it.
nd also when comes to company tax i have to pay out of my pocket?
Who knows? if they keep your vat money perhaps they will want to also look after your corporation tax money / your paye and funds to pay your personal dividend tax etc.
Feel free to send me private message if you want more standard advise, hopefully they can answer your questions and its not as you have been lead to believe.