First of all, do not be hesitant to take on a challenge. You have to believe in your abilities !

But you shouldn't run before the train either - you are worrying about stuff way too early. If that code is well documented, the first thing of course is to read the documentation. Try to concentrate on the smallest chunks - the small/simple modules. Understanding some of them thoroughly will help you build up confidence.

As others said, and you've already read, there are debuggers for Perl, and there are debugging techniques you can use. But first and foremost you must understand the system and try it on simple examples. Advance in small but sure steps. It's good for confidence and overall performance.

And if you run into trouble, always remember that Perl has perlmonks out here, always willing to help.