I would say leave CGI::Application alone until you improve your understanding of OO programming.
I was fearing that answer ;-).
I have read through perlboot, perltoot, LPORM, the relevant chapter in "Advanced Perl Programming' (which, of all the tutorials, I found to be the most helpful, followed by), the tutorial right here on PM. I understand OO to a degree, but then, I fail to understand how it would benefit me in my own application. And, because of a lack of time, I end up doing things my own way instead of taking time to learn something new. (the same thing happens whenever I sit down to learn Python -- after ten minutes or so I fail to see the point of learning something that will help me do what I can already do using Perl).
Something tells me that at some point I will have to learn OOP enough to actually think that way. Until then, I want to get with creating something with what I know, unless I hit an otherwise unsurmountable wall that can only be climbed with the help of OOP. (tilly's The world is not object oriented was enlightening). Until then, something tells me that OOP is worth it only for really, really large and complicated applications. I haven't encountered that largeness yet.
Update: I do intend to learn OOP, but I want to do that via Obj-C (I bought "Cocoa Programming for Mac OS X"). In time...
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