Installing MB-System is generally straight forward. A brief summary of the required steps follows:
Download the MB-System package.
Install GMT and netCDF if you haven't already. If you have locate these packages on your system. Verify that you have perl installed on your system as well.
Create a home directory structure for MB-System and unpack the tar ball.
Edit a copy of the "install_makefiles" script, specifying your parameters.
Run "install_makefiles" to modify the default Makefile's for your parameters.
Build the source with make, and install it with make install.
In general you do not need root privileges to compile MB-System. (This is somewhat dependent on where you chose to put package, of course.) However if you are starting from scratch, you may need them to compile and install GMT.