Thanks for reaching out to the Community, @Justin K.
At this time, there's not a way to import Check Numbers into QuickBooks Desktop Enterprise. I'm going to submit feedback to our Product Development Team about bringing in a feature that will allow this to happen.
In the meantime, here's a Community Article that provides more information about Exporting, Importing, and how to edit IIF Files for QuickBooks Desktop.
Let me know if you have additional questions or concerns. I'm always here. Have a beautiful day.