If you receive a lump payment from your client and are trying to apply it to multiple invoices across different matters but can not do this, then you have Project Accounting Isolation turned on. To learn more about the accounting isolation differences, click here.
With Project Accounting Isolation you are able to completely separate each Project under your client. When Invoices are sent out only the details and totals of that project only is shown to the client. This comes in handy if projects are sent to different companies for reimbursement under one client. When you receive a payment for a client set to Project Accounting Isolation you must choose the Client and Project that this payment corresponds with. Let's say you have three invoices, all $1,000 each. If you send all three invoices to the client and they send you a check for $3,000 then you would need to manually separate this payment to apply to those three different projects. You would go through Accounting - Receive Payment and put in the first $1,000 to Project A, another payment of $1,000 to Project B, and the last $1,000 to Project C.
If you are sending your client all invoices for each project expecting a payment for all projects together then it might be best to work at Client Accounting Isolation instead. That way you could put the $3,000 payment in and just apply $1,000 three times for each invoice to zero out the payment.