Problem: I'd like to know the best practices for using Toolset in a multisite environment.
Solution: Normally you will register Toolset once in the main Network Site and perform your plugin updates there. Those will propagate to all the subsites if the plugins are Network Activated - it's not necessary to register each subsite. At least Toolset Types must be network-activated to see the Commercial tab in the Network Site's Plugins > Add New page.