Hi there, Ecoboy101.
Currently, there's no way within QuickBooks Desktop to take out the inventory on-hand when you create an estimate. This is because an estimate is a non-posting transaction. The inventory will only deduct when you convert this to an invoice or sale.
However, you can integrate a third-party app to allow you to decrease the inventory on-hand when creating estimates. Since we're unable to suggest a specific app to use, I'd encourage you to go to Intuit Marketplace.
I also recommend visiting our Firm of the Future. This is where we share recent happenings and future developments, such as updates to newly added features.
Please refer to the articles below on how QuickBooks Desktop Enterprise allows you to set up multiple locations for tracking inventory. And, to fix issues arising from negative inventory.
Please know that you're always welcome to post if you have any other concerns. Wishing you and your business continued success.