A couple of ways to accomplish this. The critical thing is to make sure you use a different port for each server instance.
First option would be to create a separate library for each user (imho, the easiest for you since you already seem to have separate libraries set-up). Just change the library path to the ones corresponding to the libraries you've set-up.
e.g.
Code:
@echo off
start /min calibre-server.exe -p 8080 --with-library "X:\PortableApps\CalibrePortable\Calibre Library"
start /min calibre-server.exe -p 8081 --with-library "X:\PortableApps\CalibrePortable\Mommy"
start /min calibre-server.exe -p 8082 --with-library "X:\PortableApps\CalibrePortable\Kids"
Second option is to have just one big library and create a saved search containing the books you want visible to certain users.
e.g.
Code:
@echo off
start /min calibre-server.exe -p 8080 --with-library "X:\PortableApps\CalibrePortable\Calibre Library"
start /min calibre-server.exe -p 8081 --with-library "X:\PortableApps\CalibrePortable\Calibre Library" --restriction "mommy"
start /min calibre-server.exe -p 8082 --with-library "X:\PortableApps\CalibrePortable\Calibre Library" --restriction "kids"
In either of the above examples, http://<your_ip_address>:8080 points to the main library, http://<your_ip_address>:8081 points to your wife's library and http://<your_ip_address>:8082 points to the kids' library.