Invoicing using time/cost feature

We work with grants.  I need to charge partial salaries, materials, partial overhead to this grant and invoice monthly for the portion that we have spent to request reimbursement.  I am completely clear and satisfied with tagging bills, salaries, and supplies as billable.  I am completely clear when creating the invoice using my customer's account, that the tabs at the top offer time/cost as a way to populate my invoice with the items that I have pre tagged as billable.  This is all working great.  Problem is the "item" column on these invoices.  Instructions never bridge the gap between requiring an item to be entered or just leaving it blank.  When I enter an item because it is required, (example:  I created an item called "grant" to cover all situations) It obliterates the lovely information that populated when I used the time/cost feature, but it does show on the correct income line on my P&L when I have applied a payment.   Or I CAN leave it blank to preserve all of these lovely lines and save the invoice, but when I apply a payment to this invoice, it doesn't record the payment as income on the P&L.  I simply can't find where this payment goes.  It shows on my bank register, but not as income on P&L  Basically, I need to know what is the use of being able to populate my invoice with time/cost if it is erased when I apply an item to the line. I want to keep the information on each line AND have the payment to this invoice appear on an income line on my P&L