So this is my setup.

Master (root)
|______Slave (/multisites/slave/)

So what I want to do is to make /multisites/slave/ the root folder for the slaves domin name.
Right now I just have the domain name forwarded to the site and masking the original path.

So when I click the forum the url still says www.slave.com when I want it to say www.salve.com/index.php?option=com_kunena.

There probably are a tutorial for this. So direct me to one or try to explain it here.

My question really is if this can be done after the slave site is created or does it have to be done when you create the slave site.

www.master.com -> Master (root)
www.slave.com ->|______Slave (/multisites/slave/)

You can NOT use domain redirection or forwarding because this destroy the original domain name.
You must use "AddOn domain" or "Parked domain" to provide a specific path or share an existing domain.

So depending on the HTTP Server tool, this can be done.
For example, with cPanel, you have to go in the "addOn domain" to specify the slave directory.