Just posting an update as I've now gotten this reconciled on ClearBooks with lots of help.
Money > Bank Accounts - Explain an imported bank statment
Do NOT use VAT Payable to explain a BANK STATEMENT. Use VAT Control. The reason is that VAT Payable adds it to a separate section and not the VAT Control report which updates the VAT due on the front page. By the way the VAT module on the front page can take over an hour to update.
Reports > Tax > VAT Return
If the total values are off can create VAT Returns to see if the data entered in the system matches the historic VAT returns submitted.
N.B. Any Invoices line items that are just Refunded Expenses by the client should be set to EXCLUDE FROM VAT RETURN. This has been confirmed by ClearBooks.
Also, if you have already reconciled / explained a historical bank statment using VAT Control, then do NOT mark a VAT Return as Complete. The reason is that that creates another Bill allocated to VAT Payable, so then 2 Bills exist under VAT Control for the same thing. Do one OR the other.
I hope that helps someone else.
Kidnest regards,
Maria