The licenses used by Navigate and those used by Windchill are two separate things. Windchill licenses include features that begin "ptc_wnc_navigate" that grant some Navigate functionality in Windchill, and you see these in your Windchill license Management Details. These do not show up in the Navigate License Management subsytem, because they are not Navigate licenses. If you need to use that functionality for more Windchill users, you will need to talk to your PTC Sales Rep to understand what you have, what it provides, and to determine if you need more. If you want to increase users on the Windchill side and decrease users on the Navigate side, that would happen through the PTC Sales Rep.
You are entitled (as I understand it) to use all of your Navigate licenses (I can't speak to Windchill licenses) in your various PROD, DEV, TEST, QA, etc. environments. Each environment will have a Thingworx/Navigate server with a unique ID (the DeviceID), and you download a separate license file keyed to each DeviceID. There is a feature on the manual license request site that will let you include a subset of your total license seats in a particular license file, so you could divide them among multiple servers in the same environment. It sounds like you may be trying to do that.
