Thanks for the reply - you answered my question even with the little information I gave!
As you mentioned, the topology lights are out and unselectable when the Helix is plugged in via L6 Link only. They work fine when the Helix is not plugged in. However, the key part to this is configuring the amp settings by connecting a MIDI cable. By using the instructions for the v2.0 firmware update, I was able to set up Channel A using the Helix's Command Center and change models across patches as needed.
Adding a MIDI cable and going through the setup steps made a world of difference. The topology lights being unlit threw me, but after working through the parameters I've got a system that is responding the way it should, and then some.
Thanks again for the reply - getting a second opinion helped solve the problem.