Under FreeBSD, you will generally be using one of two versions of the cvsup port itself to do your synchronization; you may install /usr/ports/net/cvsup if you want to get the optional X11 GUI features, or /usr/ports/net/cvsup-without-gui if you don't plan to use X11 or otherwise don't care about the pretty windowed display (such as on a headless_server). If you choose to use the full version of cvsup, it will function precisely like the cvsup-without-gui version does if you are not running a windowing system. Please note, however, that if you don't have X installed, you do not generally want to install the full cvsup package with the gui, as it has a LOT of X-related dependencies which you utterly and completely do not need or want if you aren't running the X windowing system. cvsup also requires Modula-3 programming language dependencies.
For examples of the most common usages of the cvsup command, please see cvs.