The best way to know whether your server has been "rooted" is to be running a host-based intrusion detection system (HIDS). Unfortunately, if you're not running a HIDS now, then it's too late to install one. The proper time to install a HIDS is when the server is first installed, and before it is put onto a network.
Briefly, most HIDS work by computing cryptographic hashes of all system binaries, and storing those hashes (along with numerous other file statistics) into a database, called the baseline database. Then, periodically, the HIDS rescans your system, comparing all files in its baseline database to the actual system files.
Yes, of course, it is possible for a rootkit to modify your baseline database, which is why you need to take a copy of that database and store it separately of the server before you put the server online. Then, if you suspect you are "rooted" (and you suspect your baseline database was also tampered with), you can boot your system from the install media, restore the known-good database from your backup, and then run a scan against the known-good. It is much more likely, however, that a rootkit will not anticipate having to defeat your particular HIDS, and so you will receive a notification from the HIDS that system files have changed, indicating a probable system intrusion.
Since you were not running a HIDS, you have no quick way to determine for certain whether you have been rooted, or what system files have been modified. You could spend a whole lot of time comparing your system files to known-good files pulled from known-good installation media, but that time is most likely better spent reinstalling your system from that media. If you want to investigate how you were rooted after the fact, the best course is to take an image of your system before you wipe it and reinstall.