The same filestructure is used at vassal40k and makes absolut sense.

You have to download the module (AoS.vmod) and create a folder AoS_ext in the sa
me folder you put in the vmod-file.
Then you have to download the extensions and pack them into the AoS_ext folder.
After starting the AoS.vmod vassal recognize the _ext-folder and loads the exten
sions.
From the sight of the developer it is easier to maintain all the extensions as y
ou can push them seperatly and don't have to rebuild the whole module. So if you
have a new fraction there just will be a new extension. If there is a update fo
r a fraction you just have to update the extensionfile.
Vassal AoS is very simple to use. I miss some comfort functions as dedicated toH
it/toWound-functions as in Vassal40K but it works very good.
So for start two simple steps:
Download the AoS.vmod and put it in a folder you like (i collect all my vmods in
one folder
Create a folder called AoS_ext ([vmod-name]_ext) and download all extensions in
this folder
Start AoS.vmod