Good afternoon Becky,
Go into Check Writer like you normally would to run a check.
Select the invoice that you need to pay like normal.
***Click on the elipsis button in the "Amount" box***
This will bring up a new pop up box that will allow you to "Select Amount to Pay" and type in the 50% amount that you want.
I've attached a screen shot if it will open for you.
Good luck...I hope this helps!