There are two ways to apply payments from funds to a bill.

1. Automatically - in the Client Information under Funds you can turn on automatic payment of new invoices. If is it on then, when you generate a new invoice Timeslips will automatically apply payment from Funds to the invoice.

2. Manually - create a new funds transactions Payment from Funds. This will take money out of trust and apply it to the invoice. 

With either of these, you need to make sure that under Client Information - Funds the show on invoice is set to detail if you want the actual funds detail to show on the invoice. The payment will show when made regardless but the trust won't show unless set to detail or summary.

So I just checked on what you said. Currently the bill style is set to detail. Also, I did do the manual option when applying payments from funds to a bill.  

If you did the manual option then it should show as paid. The bill itself won't reflect the payment because the payment was made after the bill was posted. If you run another bill it would show the prior balance and the payment 

So I did just run another bill. It says the same thing -- the balance due is $990.00 and there is $5,000.00 in the retainer. Is there some setting in the bill layout that should be checked to reflect this?  

Sounds like something is wrong. I would need to see what is going on.