Well there is no easy answer on that question. As you noticed you basically asked several questions.

The main thing you need to realise at this point is that Perl is very much different (in logic) than PHP. Ah also, CPAN ... guess you already heard about it?

Also, I believe that you would benefit from using a framework. There are many, but my recommendation is CGI::Application. It's quite simple to understand, doesn't abstract too much, doesn't get in your way but gets you on the right track as it promotes using of good coding style and strategies.

CGI::Application Wiki

You might also want to check this recent node .... 518869 (CGI or mod_perl) as it gives info on related stuff.