Ok here is what you can do, create a new petty cash account called “CIS Control Account”. Once you created the sales invoice , just show in notes to invoice how much CIS is deductible (not line item). Go to CIS control a/c record receipt and allocate against this invoice you just created, then once you get net receipts from customer (after deducting CIS) allocate that against this invoice.
Your CIS control a/c will show how much you can off set against paye, end of do your normal paye journal and when it comes to paying paye, you can do one payment entry in CIS control a/c, allocate it as payment to HMRC (paye) and rest of balance in PAYE liability account can be paid off from main bank account