It's good you're using both QuickBooks and Neat to help streamline your business. I'll be happy to share more info about integrating the two together.
Based on what you've described, I recommend checking your import settings on your Neat account. It's important to confirm that your import settings are correct so you don't have issues. I want to make sure you get the right support with this, I suggest reaching out to Neat for help with navigating the settings on their program. Here are their contact details: