The CounterPoint Integrator is installed on your server. On your server desktop, you should see a blue icon labeled "Modern Retail Integrator".
This is where you have to choose which inventory locations will be used to create the sum of the Inventory Quantity on Hand value to send to the website.
If you want to aggregate other Inventory locations, you have to add the other locations to the list in Integrator Main Menu->Setup->Inventory Location window.
After you've added your locations, go to Functions>Send All Products to complete the process.
It's important to note that this process will result in an aggregation of the selected locations, not specific inventory totals for individual locations.
If you have additional questions, please feel free to submit a support request.