Allow me to step in, CaptainEon.

TaliaI is correct. The option to accept payments through PayPal for recurring invoices is currently unavailable in QuickBooks Online (QBO). 

You may want to check this link where my peer, LilyC, already answered and provided a workaround to the same concern you've posted. 

On the other hand, QBO follows the number sequence from your recurring invoice including the manually entered ones. 

I'm linking an article just in case you need help with changing the invoice number on sales forms.

Please let me know if you have any-follow up questions. I'm here to help. Have a wonderful day.