It usually uses any paypal balance automatically, before using whatever other payment type you select.
The only common exception would be with a locked or pending balance (whatever they call it), eg. if you are a new ebay seller - payments to you are held until the buyer has received the item and left positive feedback, or at least not complained and some weeks have passed.
It's to ensure new sellers are real and not scammers. Once you get a reasonable feedback level as a seller (+10?), payments to you are released straight away.
Or, if a transaction on your account has been disputed. They can put a hold on everything then, until it's resolved.
As you don't give exact details of the situation, I have to make guesses..