Best get this nipped in the bud from the out set otherwise bigger problems could lay ahead.  Imho, it also shows your professionalism that you want monies applied correctly, instead of trying to figure it out later.  I'm glad you received most of your money's, but it was not a bad idea to stop and get things straightened out early and I am sure the client would like it that way also.  Once they get on track with you, I believe things will work out.

Good luck!

Jay