One of my main complaints with APE is that the documentation is scarce and badly written. It took quite a while to figure out how to add my own serverside javascript files in APE. Note that I'm running Ubuntu 10.10, and I installed Ape through the debian package.

The path to serverside javascript files are set in /etc/ape/javascript.conf - Mine looks like this:

You'll see, when going to /var/ape/ , that the example serverside javascript code also resides there, in the directory examples/ 

So to run your own serverside javascript files, throw it somewhere in the /var/ape/ directory, and put the necessary hooks and functions in there. Take a look at some of the examples to get an idea.