How do I enter a deposit as payment towards a invoice but nothave it show the invoice is paid if there is a credit still

Start by Receive Payment and then you can manually apply just a portion of the payment and keep the invoice open. You will have remaining balance and a credit. Just ensure that you have not set preferences to automatically apply credits ( gear icon company settings)

Once the payment is recorded, if you posyed to Undeposited Funds, you can add it to other payments going to the bank.

Example: customer invoice = $100

Customer payment =$100

You apply only $80

Customer credit=$80

Open invoice =$80 however  

Open Balance =$0

Any particular reason you do not want to clear the invoice?