How can I get vendor bills for work on customer invoices to reflect internally as paid or not on the customer invoice for vendor payment tracking purposes?

Thanks for posting in the Community, @scratchmagiclv. 

Let's first turn on the Mark all expenses as billable feature in the preferences, so you can select vendor bills to add to the customer invoices. This way, it will reflect the payment status on the transactions internally. I'll guide you how. 

1. Go to Edit from the top menu.
2. Select Preferences.
3. Choose Time & Expenses from the left panel.
4. Go to the Company Preferences tab.
5. In the Invoicing Options section, check the Mark all expenses as billable box.
6. Click OK.

The screenshot below shows you the steps. 

Second, create bills for your vendors. In the Expenses or Items section, select the Customer:Job to make them billable. For more details, see the second step through this article: Tracking Job Costs.

Once done, create an invoice to apply those billable expenses or items. Let me guide you how. 

1. Go to Customers from the top menu.
2. Select Create Invoices.
3. Choose Customer:Job.
4. Click the Select the outstanding billable time and costs to add this invoice? option in the Billable Time/Costs pop-up window and click OK. 
5. In the Choose Billable Time and Costs window, select Expenses or Items. 
6. Make sure to put check marks on the billable expenses or items you want to add to the invoice. 
7. Choose OK. 
8. Click Save & Close. 

See the screenshots below to show you the last six steps. 

You can always run the Unbilled Costs by Job report to view your open billable items or expenses. Just go to Reports from the left menu. Then, select Jobs, Time & Mileage and choose the report as seen in the screenshot below. 

I'm here anytime you have other concerns. Have a great day, @scratchmagiclv. 

Our invoices are auto generated by syncing QuickBooks from a ticketing app on Android devices in the field. I then run a commission report out of that 3rd party app and create a bill in QuickBooks for the vendor that did the work. With that workflow in mind, making the bill after the invoice, is there a way to track payment of the vendor against the individual invoices they worked on?

Happy to see you again, scratchmagiclv.

Currently, the reports for show the bills and it's payment in unavailable. As a workaround, you can track the payment of the vendor by creating Sales order from the customer's side. Then you can link the invoice or purchase order in that transaction.

The transactions can be seen both to the customer's side and vendor's side.

Also, this article can be handy in customizing reports in QuickBooks Desktop.

Let me know if you need further assistance. I'll be around to help. Take care.