How many cores I am using on a Linux Server?

Unless explicitly configured not to (ie. pinning a process to a specific CPU), all cores can be assumed to be in use at all times. The scheduler will allocate processes the next available core. Case in point, "System Monitor" (part of GNOME) is showing my load almost the same across all 4 cores of my machine.

You can get a rough estimate by running top, hitting 'U' and specifying your username, and then adding up the CPU utilization of your top few processes.
You can get a rough estimate by running top, hitting 'U' and specifying your username, and then adding up the CPU utilization of your top few processes.