Would subfolders pointing to a diff domain conflict with ISPconfig installation?

Good Morning,

I have a question regarding, ISPconfig, I followed through the tutorial (https://www.digitalocean.com/community/tutorials/how-to-install-ispconfig3-on-an-ubuntu-14-04-server), it’s up and running.

Unfortunately, i didn’t make this installation on a blank droplet, i used my old one which was modified to take subfolders domain (EX: site1.com /www/site1.com and site2.com /www/site2.com).

My configuration is something similar to this:

/etc/apache2/sites-enabled/000-default.conf

<VirtualHost *:80>
    DocumentRoot /var/www/site1.com
    ServerName www.site1.com
    ServerAlias site1.com
</VirtualHost>

<VirtualHost *:80>
    DocumentRoot /var/www/site2.com
    ServerName www.site2.com
    ServerAlias site2.com
</VirtualHost>

/etc/apache2
apache2.conf :

ServerName www.site1.com 
ServerName www.site2.com 

Problems are the following, and I don’t know which way to go about it,

First, should i add my server.site1.com subdomain to apache2.conf and 000-default.conf? [The only reason why i used subdomain was because tutorial did, should i just point to www. domain?] (https://www.digitalocean.com/community/tutorials/how-to-install-ispconfig3-on-an-ubuntu-14-04-server)

Second, the site2.com, Should I erase it from my apache configuration files and let ISPconfig recreate the configuration by adding a new user and site?

Third, I am able to login to panel using either domain, is there a way to only allow to access panel through site1.com:8080? instead of both.

Thanks for the help and recommendations! Digital Ocean Rocks \m/