Paul, start a startup.m file and store it in your main matlab folder. From the documentation,
"At startup, MATLAB automatically executes the matlabrc.m file and startup.m, if it exists on the MATLAB search path. The file matlabrc.m, which is in the matlabroot/toolbox/localfolder, is reserved for use by MathWorks® and by system administrators on multiuser systems."
In your startup.m file, add all necessary paths to run your scripts, functions, and other files that matlab needs access to.
Next time (and every time) you start matlab, the paths will be added automatically.