The Perl Debugger (perl -d) is your friend. The 'm' command reports on the various methods available to an object; use it just after you have instantiated the beast --

my $obj = Class::new();
  DB<1> m $obj
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'T' gives stack trace information and tells the context the routines are called in. I also use 's' step into method calls and then explore with 'w' and friends to see where I really ended up.

In terms of graphics, I have yet to find something that beats pencil and paper for the fine detail, white-board and Visio diagrams for the over-all structure. And Document Everything! Build POD, ReadMeFirst files, Twiki pages, what ever make you comfortable. Even if you don't have to come this way again, someone else will.