SubDirectories Versus Subdomains Which Is Better? How to Create them by ISPConfig?

Earlier i had my home server set up on opensuse 13.2. I was managing it without any control panel by modifying files manually. Later on i started using 'monit' and liked it. Now I want to try ISPConfig control panel to create my website from scratch. I have few questions:
(1)On opensuse 13.2 (without using ISPConfig) my directory structure was as below:
Web root: /srv/www/htdocs: The index.html page inside htdocs was accessed by http://magicbits.net
Moodle: /srv/www/htdocs/moodle Accessed in browser by http://magicbits.net/moodle
Wordpress:srv/www/htdocs/wordpress Accessed in browser by http://magicbits.net/wordpress
..........and so on for other PHP-MYSQL solutions put inside "htdocs"
Here i faced one problem: My SSL certificate was for "magicbits.net" and browser was showing warning when a person typed URL -say- magicbits.net/moodle. WOULD A WILD CARD SSL CERTIFICATE HAVE SOLVED THIS PROBLEM OR DO I HAVE TO BY DIFFERENT CERTIFICATES FOR "magicbits.net" , "magicbits.net/moodle", "magicbits.net/wordpress" .......... and so on?

(2) Now that i have successfully installed ISPConfig-after replacing OPENSUSE 13.2 by UBUNTU 14.02 LTS server- i want to try the sub domain approach i.e. I want my sites to be accessed by "moodle.magicbits.net" , "wordpress.magicbits.net", "webmail.magicbits.net"... and so on. CAN SOMEONE GIVE STEP BY STEP METHOD TO DO THIS BY USING ISPConfig CONTROL PANEL? I think it is done by creating virtual hosts but i am not clear in that area. I also want to know if i have to purchase different SSL certificates for "magicbits.net" , "moodle.magicbits.net" , "wordpress.magicbits.net"......etc or there is a way to use a single certificate for all?

(3)Can someone suggest which out of (1) and (2) above is better for a single site on a home server? Any third better alternative is also welcome.
Sorry for rather long post but i tried to give maximum details. Thanks in advance to all.