MPI is a programming library that is used to write parallel programs. In general, programs must be explicitly written to use parallelization. I work with clusters on a day-to-day basis and let me say this tends to be harder than it sounds. In your case, you would need to write a special program to chop up your input files into chunks, distribute the chunks to all your computers, and reassemble the result. This is probably too much work for your app (though it works nicely with the scientific apps I work with), but from the post above, it looks like someone has done the work for you, so you're golden. An easier way, if the program above did not exist, would be to encode three files at once, one on each computer. This is what Mosix can do for you. Mosix migrates CPU intensive processes to the computer with the lowest load, thus balancing things out.
I'd suggest taking a look at www.beowulf.org
for some information on clustering.