You'd use the Undeposited Funds process for this, so effectively:
Receive Payment of full invoice amount, post to Undeposited Funds.
Record £10 expense, selecting Undeposited Funds as the account to pay out of.
This will leave £90 in Undeposited funds. Create a Bank Deposit, select the Invoice Payment and the Expense (Select £100 & £-10 = £90), with the total Bank Deposit at £90, make sure the Date of the Deposit matches what is on the Transaction on your Banking section. With the date, and overall amount being deposited at £90, you should