I am assuming you are creating the invoice and asking for the deposit to be paid, not that you already have the deposit and wish to apply it to the invoice.

I don't know of any way to enter it at the bottom of the invoice as you have indicated unless you have already received the payment.

I would use the last line of the invoice and enter the request in the Description column.  I enter the dollar amount in the Price column and do not enter a quantity so that it will show on the invoice formatted as a dollar amount properly but not get included in the totals.

When I want to add a note or comment I put it in the Comment Box on the left hand bottom side of the invoice.  Works great.  It won't keep that message after you post, it will revert back to whatever you have set up in settings. If you already have a message in that box you can safely change it on the fly and once you post it will go back to what you had in there before.