Linking Payments from QBO to OMS
Overview
Whenever we receive a payment in QuickBooks Online there is a Zapier automation which grabs the relevant information (Most importantly how much was received, and which invoice it was applied to) then creates a communication note in our Opening Management System with that information. It then searches the Site Visit, Counter Ticket, and ToQBO Reoccurring Charges (subscriptions) tables and links the comm note to the record that matches.
This is a nearly automated process with 3 notable exceptions*;
1) Payments for an invoice with a "-#" (e.g. 218250-1);
2) Payments made via credit memo(s);
3) Payments for Lab invoices (If someone pays invoice 1246, OMS can't tell if it belongs to the Lab Project "1246", Site Visits "221246", or "C201246").
*There is a bug where sometimes a "regular" payment doesn't link at all. This usually happens if two payments automate at the same time; one will get a timeout error and won't link anywhere.
Manual Process
(Video at the bottom)
There is a queue on the Collections dashboard called Unlinked Payments. Any Communication Note that is type "Payment Received" and is not linked to a Customer and SV/CT/RMR/Lab will populate here.

You must use the amount and reference number to determine where this payment should be linked. In the below example, you can see that someone attempted to pay $300 for M104589.

You then confirm in QBO that this payment is legitimate and should have been linked.

Finally, add the appropriate relationship.

This is a video of linking a split invoice and a Lab project.