Few beginner questions

My host technician has recently emigrated and I'm left managing my Linode which I've had since 2010. I'm not very Linux literate, but I have learned basics such as setting up php, mysql, apache, virtualmin phpmyadmin etc, and have vowed to teach myself how to manage the hosting of our sites myself.

So, I was having a bit of a tidy up on my Linode (1GB Ubuntu 10.04) as I host 22 domains, and noticed a number of issues my tech hadn't done for a while; no updates using apt-get on Ubuntu for months, phpmyadmin quite an old version etc. I have gone ahead and updated and sorted out any niggling conflicts this has created. I have also made my domain fully qualified, something else which wasn't previously done!

However, since making the domain fully qualified, I've noticed that the FQDN is pointing to an empty directory (http://elise.sienco.co.uk) and I cannot work out where to place files for this location. I know this isn't necessary, but thought it would be nice to have a landing page to my FQDN or a php info page or something.

Also, my tech has set up the linode mostly with sub-servers. There are 4 virtual hosts, and lots of sub servers off of all these (each of them a different client). I'm struggling to work out why this was done. Most of my clients don't have any access to their sites (FTP or otherwise), so I'm thinking it was just out of laziness, but I'm wondering if there is any merit in doing things this way. If not, is it easy to move sub-servers to become virtual hosts, or will this cause issues?

One final issue. I have just created a new virtual host for a client who requires ftp & database access. I believe I set all up okay. However when I went to the public_html folder on their host and added a holding index.php page - nothing showed up on their domain and instead a file is downloaded. If I change this to a html file all is okay. Has PHP not been enabled for this domain? If not how should I have done this? My server has index.php defined in the DirectoryIndex (in /etc/apache2/mods-enabled/conf.d) and it works on all my other virtual hosts and sub servers.

Sorry for the random questions all in one post, thought it better to keep them together.