It would help if I had a full breakdown of which sets you have.
Having both InteriorWorks sets helps...they’re VERY flexible. I’d personally recommend printing out a fair number of regular stone tiles sufficient to cover a sheet of foamcore to create your “masterboard”, and then just utilize an assortment of wall sections...some large, some small...and use the recommended “clip-it” system. It works really well for creating on-the-fly rooms and corridors using the WWG materials.
While I find the 3” walls of the modern sets to be a pain sometimes, the 2” walls are rarely a problem, and don’t get in the way at all. What they (and particular a good assortment of props) DO do is create a very visible, interactive environment. You can mention a chair in the description, describe it on the whiteboard, but I’ve found that players are far more apt to interact with their environment if it’s physically THERE...if a player can SEE the cardstock crate in the corner, the character is much more likely to pick up a crate and hurl it at a foe.
As a general rule, though, I find that it’s far easier to adapt settings to the card, instead of trying to make the card strictly adhere to the layout of the setting. You can do it...you can make the rooms, corridors, etc. exactly the way they appear on the map...but it’s not always worth the additional effort. Sometimes, it’s better to find a compromise between the two and focus on just the tactically-critical layouts being exactly as-is.
For an example, many D&D modules depict round towers. If the octagonal tower from CastleWorks Ultimate is about the right size, I’d just stick with the octagonal tower instead of trying to recreate the round tower.
As mentioned...if you can get me a list of the other sets you have, I’d love to take a look.
And if you’re interested...WWG also has a few 3E modules on their shelves, with all the foes represented as standees, added models, and extended support for the sets designed to make use of them (including two written my yours truly).