I'm not sure if I'm understanding your problem correctly so please correct me if I'm wrong. It sounds like you have the following configuration:
Main site located at http://domain.com
Secondary site at http://domain.com/folder
Am I correct to assume that you're having an issue installing WordPress on the secondary site when you have WordPress installed on your main site? Are you getting a 404 not found when your secondary site redirects you to http://domain.com/folder/wp-admin/install.php or did you already pass all of that part?
If passed, IGNORE THE REST and please clarify my confusion if you would like me to help you. Email [Redacted]
If you are having that issue, here's a suggestion on what you can try, which worked for me. In your root directory, you will see your .htaccess file. In that file, near the top, look for this:
Deny from all
For now, change the Deny to Allow. This will allow you to install WordPress on the secondary/tertiary, etc. After it's installed, it is crucial that you change it back to Deny. You can then browse your multiple WordPress instances.