This is no problem, and just about anywhere you get a VPS, dedicated server, or other, they are going to install some default that they have for you. My service provider was good enough to allow me to tell them how I wanted it installed. If you can do this, just ask for the basic system with an ssh server.
It doesn't matter though. If they provided you with something already, just use this howto: http://www.howtoforge.com/perfect-se...ispconfig-3-p3
, starting on page 3 as I marked and follow. In general, you should be fine. If a package is already installed, it won't reinstall it, and things that aren't installed will be installed.