no it's just a question of the executable not being in your path. Path is a system wide variable for where the command line looks for its executables.
so say you have a program in /opt/bin and the shell doesn't know it has to look there it will mean that you need to enter the absolute path to the program as in /opt/bin/nano, if you add /opt/bin to the PATH variable via a .bashrc script (this script gets run every time you login) then you will be able to just call nano and /opt/bin/nano will get executed.
to link /opt/bin/nano to /bin/nano just do the following:
ln -s /opt/bin/nano /bin/nano
as /bin is already in the search path, then you will only need to call nano on the command line and it will execute the linked /opt/bin/nano.
the better solution of course is to use a .bashrc script… look somewhere in the thread about optware I've posted an example. this way you won't have a bunch of links lying around the drive, and it will be a lot cleaner when you decide to uninstall things.