Hi. When we receive payments from Jobber (or any other integrated system), should we match the bank transaction to payment or to the correspondent Invoice?

Hi there. Glad to have you as a new member in the Community. I'll be happy to share more info so you're on the right track with your work. 

Categorizing your transactions the right way is essential for ensuring your books remain accurate. That said, I recommend consulting an accounting specialist for expert advice. This ensures your entries are recorded in a way that allows for you to navigate the program with peace of mind. You can get in touch with an accounting professional using this link here. Other accounting professionals are able to see this post in the Community and this will allow them to chime in. In the meantime, feel free to check out this article that shows you how to:  Categorize and match online bank transactions in QuickBooks Online. 

Let me know if this info helps. I'm here to steer you in the right direction.