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Yes, you can indeed use Shipping Manager in QuickBooks Desktop without relying on ShipEngine. Let me share more information and address all your questions one by one.
Since you've negotiated your own rates with FedEx and UPS, you can directly utilize those rates within QBDT's Shipping Manager. You'll need to configure your carrier accounts with your negotiated rates within the Shipping Manager settings. This will allow you to generate shipping labels and track shipments using your pre-existing agreements.
You mentioned your workflow involves shipping first and then creating the invoice with tracking and cost information. Here's how you can handle shipments before invoices:
Regarding the continuity of your current shipping screens after May 31, it's important to understand the implications of discontinued QuickBooks Desktop services. For QuickBooks Desktop versions that are discontinued, online services will cease to function. However, if you are utilizing a supported version of QBDT, such as QBDT 2023 or earlier, you will still be able to utilize the core shipping features. Additionally, here's an article about shipping manager with frequently asked questions in QBDT: Intuit QuickBooks Shipping Manager.
For in depth and specific configuration of your shipping setup, as it involves privacy related information, I would strongly recommend contacting our QuickBooks Desktop Support team. They can provide detailed technical assistance and ensure your shipping setup is configured correctly based on your specific needs and QuickBooks Desktop version.
Moreover, you can also consider setting up and managing your inventory as it can help with your shipping, let me add this article as a reference: Set up Advanced Inventory in QuickBooks Desktop.
Let me know if you have additional concerns besides shipping management in QBDT. I'm always here to help.