WHMCS Admin → Client → Invoice → Add Payment (tab)

• Payment Method → Mail In Payment
• Transaction ID → Check number or other ID
• Amount → Payment amount
• Send E-Mail → to client, or not
• Add Payment

WHMCS Admin → Client → Create Add Funds Invoice

• Amount → Amount of partial payment

WHMCS Admin → Client → Invoices → Open the Add Funds Invoice → Options (tab)

• Payment Method → Credit card or PayPal
• Save Changes
• Attempt Capture

Once the credit is in the system, apply the credit to the invoice:

WHMCS Admin → Client → Invoices → Open the Add Funds Invoice → Credit (tab) → Add Credit to Invoice

• Amount
• Go