There are two ways you can account for fees deducted at source for your Sales.
The first option (more detailed but also more time consuming):
Issue the invoice in Crunch for the gross amount;
Record the client payment as paid into the bank account for the net amount you received, and allocate this to the invoice;
Record a second client payment for the fee amount, and set this as received personally then allocate this to the invoice, and;
Record an expense for the fee amount as paid personally.
This method means the invoice will show as fully paid, but you also have a way to record the expense without it affecting your bank reconciliation.
The second option (Recommended - simpler and quicker, but doesn’t include breakdown):
Issue the invoice for the amount received, net of fees, and;
Record the payment matching the amount you received into the bank and allocate to the invoice.
This method means you don’t record the expense for the fees but, as the total invoice amount has been reduced, the impact on your tax is a net effect of zero.
Please note that this may not be suitable if your company becomes VAT registered so please seek further advice if you register for VAT.
Crunch does have it in their roadmap to make this a smoother journey.
Hope this helps.