I have installed phpmyvisites on a website which has subdomains (http://subdomain.domain.com). Do I have to do something special to make it work with phpmyVisites? Do I have to set the alias for all the subdomains?

It actually depends on what you want to obtain:
- if you want all your statistics to be recorded under the same "website" in phpMyVisites, you need to add the same javascript code to all your subdomains. You can also add the alias in the administration, but this is optional (it will be useful for not to display the URLs in the referer section).
- If you want to have the statistics of each subdomain in a separate website in phpmyvisites, then you have to create these websites in the administration, and add the code to your subdomains (be careful, the code is then different for each subdomain!)