How do you record a bond payment that is deducted before you are full invoice amount (which also has CIS deductions)?

We have a retail kitchen company that we provide kitchen fitting services for (as a sub-contractor under the CIS). They want to retain a £1000 bond from ourselves but have agreed that they will deduct a £40 bond payment from each of our invoices until the £1000 has been reached. The bond will be returned as a later date (or if the contract is terminated etc). Currently we send them an invoice with a CIS labour standard 20% service amount on it. The company deducted the CIS on this full amount and then deducts £40 before paying us. Eg Full amount = £1682.29. CIS amount deducted (20%) = £1,345.83 £40 bond deducted: Money paid to us = £1,305.83 How do we set up our invoices / accounts to when we receive the payment of £1,305.83 it matches our invoices? Also, how do we keep a track of the £40 deductions so we know how much the kitchen company has in terms of bond money from us?