First off, welcome to Perl Monks prairie dawn. Now to try to answer your question. You will find out that TMTOWTDI (There's More Than One Way To Do It) so I'll throw a few ideas at you, and I'm sure that the other monks will as well. Take the best from all of us and keep us informed of the progress. I think this answer comes in two steps, the first one is Off Topic (design), but the second is Perl. I'll cover both of them briefly.
The first suggestion I have is not in perl, but in design. The elements that you are comparing to at Perl Monks, are all laid out in a similar manner so it's easy to customize what goes where. For example, if I want to change the position of the Chatter Box, with my Personal Nodelet, I can because they are both on the right hand side with the same design elements (width, color scheme, etc.) So you will need to design all of your elements so they are interchangeable. This is step one. Do numerous mock-ups in HTML and make sure that all parts are interchangeable.
The Perl answer (or at least one of them) is HTML::Template module. You can seperate your perl from your 'design' and in the Template, your design has some basic if logic, loop logic, and can pull in variables from your Perl. I suggest that you start your research (at least the Perl side) on HTML::Template and keep asking questions posting code where you are having troubles. Good luck.