Hi Jose Pablo,
In oacs-5-2 you have in DefaultMaster param the value "/packages/dotlrn/www/dotlrn-master-custom", with this file you can get the idea to replace the master.
You can set a site-template for each user, maybe you can change the site-template when you are inside your application and restore the old site-template when you exit.
Each community has its own template too.
Regards,
Héctor