Turning estimate into invoices. Why when I am turning and estimate into a partial invoice at calculates the percentage before gst and then adds the gst after.

Hello robbie2,

Welcome to the Community. QuickBooks offers a powerful tax module that simplifies the way you manage your taxes. It's important you know how the calculations work in QuickBooks and I'll be glad to share more info.

The program does the rounding by two decimal places and I encourage you to check out this helpful article that explains more about how rounding works in QuickBooks: 

Tax Rounding off logic in QuickBooks Online API.

Let me know if this explanation helps bring things into perspective. You're more than welcome to reach back to me in the comments below if you have other questions.