The balance sheet is a simple view of charges and payments.
It is a client selection view like To Dos and Invoices. You need to select the client on the left side of the ProfitTrain window and then you will see charges and payments for that client only.
On the lower bar you have buttons to add new payments or charges and the client balance in the far right. Line items can be edited by double clicking the field and making your change.
Usually invoice payments are made from the Invoice view where you can apply the payment to the invoice and change the invoice status at the same time. There are times when making the entries directly on the balance sheet are best though. Maybe you have a retainer from the client that you are working off. You can enter the payment here and then manually mark invoices as paid by changing their status.