I am new to virtual hosting. In the past I have had one website per server and evrything went into /var. It appears however that with virtualmin they go into /home/site. Is this acurate? Also do MYsql data bases still go into /var or would each sites database live in /home/site.
Howdy,
Websites do indeed go in /home… that’s because each website is associated with a users account, which also exists in /home.
MySQL databases would go in /var/lib/mysql. That’s because they aren’t accessed directly like files for a website… instead, users access their database information via the MySQL daemon.
-Eric
All of which can be configured of course to have the stuff go into other directories. 
Though if there is no real reason to do that, the defaults work nicely.
One reason to e.g. move the MySQL databases elsewhere, in my case to /home/mysql, is that I have a RAID-1 partition for /home for data safety, whereas the / filesystem (including everything except /home) is a non-RAID partition.