I have a project called cityscapes:
http://net18reaching.org/net18/cityscapes/doku.php
Each of the 18 countries listed there is an independent wiki, all sharing the basic Dokuwiki engine. It is on a Linux system, and uses symbolic links. So, if you are not using Windows, this can easily be done. If you are, then you can create the equivalent of symbolic links using the Winbolic software. Here is the structure of a typical top level directory:
bin -> ../map/bin
conf
data
inc -> ../map/inc
lib
index.php
doku.php
feed.php
The lib directory looks like this:
exe -> ../../map/lib/exe
images -> ../../map/lib/images
plugins -> ../../common_plugins
scripts -> ../../map/lib/scripts
styles -> ../../map/lib/styles
tpl -> ../../common_tpl
You will have to assign your own links, of course, but this indicates the principles. Each user gets a separate data and separate conf directory. Everything else is shared. The parent (farmer in local parlance) is 'map'. And since I didn't want the children (animals) to have access to map's tpl and plugins, I created a separate directory for the children.
I might also add that this is all automated. if someone from a new country enrols in the project, a new wiki is created.
This is not the kind of setup you would use if you had independent users, all with admin privileges, but that doesn't seem to be the case for you. That is, they are all wikis run by you, so they can all be administered by a single administrator from the main admin panel -- which in the above case would be 'map'.