The easiest option is to turn the script into a function, and then put all of the other functions in the same Mfile. Doing this is easy, reliable, and it gives you exactly one simple Mfile.
With MATLAB it is not currently possible to mix scripts and functions in one Mfile, so you cannot simply place all of those function at the end of the script. But it is easy to convert a script to a function, and then you can put all of the other functions in the same file. The first function is the one that can be accessed externally by calling the its name, all of the other functions can be called by any function in that file (called local functions).
You should really be writing functions anyway: scripts are great for playing with code, but not for writing serious code (especially not code that you will be distributing to others!). This is because functions each have their own workspace, letting you encapsulate your algorithm without it being disturbed by the calling workspace, and vice versa.
