Hi Jonathan
You are indeed correct - balances owed to HMRC should not be listed within trade creditor/debtors. Unfortunately, it's the way ClearBooks has designed the system due to everything relating to 'bills'.
The VAT situation can be changed by heading to Settings > Toggle > Accounting > VAT return journal (tick) - this will then create a journal to a specific VAT control a/c instead of lumping it into trade creditors (if you do this the way you subsequently analyse the payment to HMRC VAT from your bank a/c will change)
Payroll unfortunately is a pain. I presume you're using ClearBooks to process the payroll? The best you can probably do is process the payroll like you normally would, find the PAYE bill the system creates, delete it then replace it with a journal analysed to a PAYE control a/c (that you'd need to create by heading to Settings > Codes > Create).
An easier workaround in my opinion is simply for your accountant to be wary of the fact PAYE/VAT balances are lumped into trade creditors and have them make the appropriate adjustments when drawing up the accounts.