Marybeth Murphy: When they order, I then go into QBO to add them as a customer and create an invoice for them.
Hi Marybeth,
Just a quick adjustment to your process to fix this - when your lead is ready to order you should create their invoice from Method and make sure you disable Wait for sync approval. When you issue an invoice to a lead with this option disabled it'll automatically convert the lead to a customer. This saves you from creating a duplicate customer record in QBO and having unlinked activities from their lead record.
Marybeth Murphy: Is there a way to merge these two accounts when this happens so that all my customer information is under one name?
We don't recommend doing a customer merge as the feature is unsupported with QBO's "IPP" (Intuit Partner Platform). Your best best is to follow this article to delete the customer from QBO and recreate the invoice for them on the correct record.
Please post back if you get stuck anywhere.
~C