Sorry, another really unhelpful response from Intuit...  The question was essentially "I'm having to create a journal entry for every one of these, there has to be a better way to do this" and the 'answer' was "Here is how you create a journal entry, and you should talk to your accountant".  Thanks but that doesn't seem to help...

Seth do you have the PayPal app installed so that it brings them in automatically?  I have that and it brings them in, but then I have to go to details and then change the item type before accepting in order for it to categorize to the right place.  It's a step, but it's not really that bad, just a couple clicks and easier than doing journal entries for each one.  Hopefully that helps.