It may seem alot more complicated, but even though there are several templates per script it will end up being a lot easier, especially for PERL novices. The reason being is without templates the HTML is buried in ifs and elses, and it's spread out over various portions of the script. With templates all of the HTML for that portion of the script is in one place.
Your thoughts about 1 template per script is something that I had wished for as well. But, unfortunately, it's not the way the FastTemplate module works. Maybe someday I can write my own to do something like this. It's highly possible, because I never really thought there was a chance to do templates period a couple of weeks ago.