Hello there, thrive_accounting.
I appreciate you for being detailed about your concern. I'm here to give you some answers to your questions.
First, manually entering amounts owed to the business will not create any issues with duplicates in the Profit and Loss report. Additionally, billable expenses will remain pending if you don't apply them to an invoice. You can uncheck the Billable column if you have no plans to link your expenses to your invoices moving forward. This way, they'll stop appearing on the right panel when invoicing a customer they're associated with.
Check this guide out to manage your billable expenses: Remove a billable expense charge in QuickBooks Online.
For future reference, click this link for more info about managing your money-out payments: Pay expenses and bills.
Please leave a reply if you have further concerns about billable expenses. I'm dedicated to helping you out. Stay safe, and have a great day!