Nope, there's no way to automatically do this. You can see what the leftover is on the Prizes page (don't "share" the leftover). But you can't sweep that into a rake, for example. You'll just have to note the leftover amount and keep track of it manually.
If you see that you have a leftover $15, for example, and then go set the "Fixed Rake" to be $15, you'll find that you've changed the prize pool, which in turn will change the % amounts that get calculated for prizes. So in the end you'll probably have to do this manually.