Hello, genesiscarpet.
I have a couple of reasons why those checks won't show up under Payments.
One prime reason is that those checks are likely filtered. Make sure to set the filter options to show the checks. In the Payments section, set the settings to All.

This will show all transactions made under that contractor.
Another reason is that those checks might've been recorded under a different profile. In this case, run a Check Detail report to find them.
Here's how:
- Go to the Reports tab.
- Search for Check Detail in the box.
- Find the checks in question then select them.
- Under Payee, change the profile to the correct contractor.
- Hit Save and close.
These articles also contain helpful information on fixing transactions for the 1099 form:
If you need to file your contractors' 1099 forms, you can read this article for the complete guide: Create and file 1099s using QuickBooks Online.
Do you need assistance doing other processes before taking care of your taxes? Check the out the guides in our general help page.
I'd be more than happy to offer assistance again in managing your contractors. I'm also open to questions regarding QuickBooks Online.