1. Apache takes over the permissions on the files for the template when template is installed.
A: Talk to your host about this if they can change setup on the server.
2. Modules are installing and are visible on the server but they are NOT coming through the Admin Panel. I cannot view the modules at all through the Admin,
Also, I cannot re-install the modules and I cannot delete the modules via FTP – even though I changed owner and groups on those files. ( I am running on Linux. )
3. Configuration changes are not taking place on the modules I can see.
Got to the admin panel, Help>System info> Directory Permissions and see if the files/folders is marked writeable.
Which host are you using?
Joomla version?
4. Can we use modules from other templates on this template?
Yes