There are various situations when you may have to apply a credit in ArchiOffice/EngineerOffice.
If you want to reflect a retainer payment and credit the project for it:
1. Go to Projects > Billing > Transaction.
2. Click New to create a new transaction and enter a Date for the retainer.
3. Choose the Retainer option to indicate you are making a ‘payment’ from the retainer account. You will be prompted to make a payment from or to the retainer account.
4. Select From to take money from the retainer account. This will display the entire balance of the retainer in the 'Amount to Apply' field. You can change it to a lesser amount, if required.
5. Enter Notes to explain what the credit or retainer is about.
6. Now click Projects to list the projects assigned to the billing client. Click Apply against that record.
7. This applies the retainer amount to the project with an “RT” code signifying Retainer Transaction. Click Done.
If a client paid extra amount and you want to reflect a credit:
This situation occurs when an invoice has been paid by the client but with an overpayment. At the time of payment, the paid amount is greater than the amount owed.
1. Record a payment transaction for the invoice as normal ensuring the Payment option is selected.
2. The Amount of payment (say $1002) will be greater than the amount owed (say $1000). Hence, enter the correct amount in the 'Amount to Apply' field. There will be a balance of the extra amount (say $2).
3. You must record the extra amount as an overpayment to the project rather than invoice. Click Projects to list the projects assigned to the billing client. Apply the extra amount to the project as a payment.
4. Click Done. The next invoice after this payment date will reflect the overpayment in the project balance.
If you want to apply a credit for services on an invoice:
This transaction is similar to others, except you will select the Credit option instead of Retainer or Payment. In the Notes section, describe the credit transaction. You must enter the Amount of credit to be given and apply that to the project. Once you click Apply, you will be prompted to select an account to allocate this credit. Typically, users select Credits or Client Fees. 
Again, the next invoice after this transaction will reflect the credit in the project balance. If you want to show a credit on the project, generate the summary report from the Projects > Billing > Options screen.