Thanks so much for the response Angelyn,

So I tried setting it up as you advised, but I still seem to be running into an issue.  Once I've invoiced for work that hasn't been done, we work on the project and we apply hours worked towards the project, it's not going to show that initial deposit as going towards the hours worked as a credit on their account.  It just shows up as a paid invoice instead of a credit towards the work that we need to do.

Thanks for your advise.