Creating an extension is very much like creating a module. It just uses a different editor that displays the base module you want to extend.
Since it extends the capabilities of an existing module, you can’t remove any functionality from the base module, only add to it. For example, if there’s a map in the main module, it will still be part of the game if you create an extension. There are also other things that you can’t do in an extension–you can’t add new sides to the game in an extension, for example, or add new traits to pieces in the main module. But an extension is ideal for adding new maps and new scenarios.
To create an extension for a module, in the module manager, right-click the module and pick New Extension. The extension editor opens (it will say Vassal Extension Editor at the top). This interface resembles the regular Module Editor, and should look familiar from creating modules, as it sounds like you have already. You’ll see almost all the same controls. However, what will be displayed is components from the main module, grayed-out because you can’t edit or delete them. However, you can add things like new maps, new pieces, new charts–click around a little to see what you can and can’t add. You can also copy components from the main module, and then paste and edit these as you need. This is a quick way to create similar components from the components in the main module.
It sounds like what you want to do is have the main module with just the common units palette, and then create new extensions, each with a new map window that displays a new map. You can add setups to the extensions just like you would with a module. Players would be able to pick and choose what extensions to load for a given game session.
After you’ve worked up the extension in the extension editor, adding your components, click Save, and save it as an .vmdx file. (As ever, it’s a good idea to save your work often.)
You need to activate an extension to use it or test it (because you’re going to want to test it), as described in the User’s Guide (right-click and pick Activate). Once you’ve activated it, you can also launch the extension editor it by right clicking and choosing edit.
That should at least get you started with the basic process.