Setting Up Two CI On One Server

I'm having a bit a trouble setting up two CI on one server.

Currently I want my application to do this:

www.example.com will run the main CI application
www.example.com/app2 will run the second CI application running on the server.

Currently I'm thinking that my directory structure can be this

/var/www/html/application1
/var/www/html/application1/app2

That way when I visit www.example.com/app2 it will automatically run the second CI application.

All is currently working well except for app2.
When I visit www.example.com/app2, it will visit the first homepage of the CI application but after I log in it will remove the subfolder URI
It will be like this www.example.com/login/tryLogin which will be a 404 Page Not Found since it needs to be www.example.com/app2/login/tryLogin

I added the base URL to be http://www.example.com/app2/ in the config file. But it keeps replacing app2. I'm thinking it might be my .htaccess to remove the index.php but I did a quick test to not have a htaccess but this issue is still the case.