First you must fill out how your character's template at 50 will look like. Only fill in as many specs as you will actually train in.. leave everything else blank. The leftover boxes are there for classes that have a large number of lines they can spec in. The parser will "fill up" your specs from left to right. What this means is that it will put points into the leftmost spec first, and work it's way right until it runs out of training points.
Nerd notes: This script works with a "brute force" method. It basically examines your template for level 50 and calculates what percent of max spec each of your spec lines will end up at. Then for each level it tries to spend as many points in each spec line as it can without actually running out of training points, or going over the level 50 percentage. Obviously this method won't suit all classes but then again this utility isn't intended to set in stone how you spec your character. ;)
You can download the code for this tool right here.
Report any bugs or send any suggestions by emailing me at gro.h7urt@rehtes after you reverse the characters in my email address. Spam is bad. ;)