If I transfer bulk payments from Paypal to my bank, what is the right way to disperse that lump some from uncategorized asset to the invoice?

I am not sure I understand your question. As an example are you just transferring money earned in your PayPal account to your regular checking account? Are you not reporting income in the PayPal account and want to record it when you transfer the monies?

If you are just transferring monies between accounts it is entered using the two bank accounts as either a deposit or withdrawal (only 1 entry please).

If you do not have the PayPal account on your books and have not already declared the receipts as income the entry would be a deposit against income.

My guess would be that you did not make the entries in QB, instead a transfer was created in QB related to connected bank accounts. I generally DO NOT use transfers at all because they limit the ability to correct an entry.   

If this solves your issue please mark as solved so persons answering questions can skip this question and move on to another question where an answer is needed.

You can adjust the rules so the bank downloads make the entries correctly. If you have both bank accounts connected to QB consider using an "Exchange" account and having both the entries post to the exchange account. 

If this solves your issue please mark as solved so persons answering questions can skip this question and move on to another question where an answer is needed.