I suppose that if you were to mark the nominal that refers to the CIS bank account on your chart of accounts as “allow this code to be used on invoices” then you could create an invoice like
| Work I did (General Sales) |
1000 | 20% VAT | 1200 |
| Less: CIS deduction (CIS deductions) |
-200 | No VAT | -200 |
| Total NET | 800 | ||
| Total VAT | 200 | ||
| Grand total | 1000 |
(If the “work I did” was split over several lines and you want a sub-total before deductions then you’d have to add that up manually and use a comment line, which is less than ideal but still works)
This would put the correct amounts of £1000 on your general sales on the P&L report, £200 “money in” on your CIS bank account, and £200 to the sales tax control account as normal. The only thing you would have to fix manually is that QuickFile calculates box 6 on your VAT return from the net invoice totals (800, in this example), so you’d have to manually adjust box 6 to add back the CIS deductions.