As you have most likely noticed, LanSurveyor Express is fairly simple. Unfortunately, it does rely on Visio for the mapping process.
The good news is the full version of LanSurveyor does not rely on Visio and is much more flexible. It also has the ability to export to Visio if needed. I would suggest downloading a trial here. Wish there were more I could do.
It sounds like a difficult scenario. What is the specific feature or question you are asking?