One of our customers has given us a down payment check for 3 separate jobs we are working on. Because there are 3 different invoices, I am not sure how to apply this check to each invoice. The down payment is 50%. I know that you can apply payments to multiple invoices to PAY IT OFF, but can you apply a percentage of multiple invoices with one payment? Or do you need to break it out somehow. I hope that makes sense.. because I have no idea how to do it.
Thanks in advance! :)

The easiest way out is to merge all the dealings with this customer into one account.
Then your problem will be automatically solved.