I use GUI builders from time to time.
I beleive any GUI builder makes quite good by helping user, but you must not require from it doing things that it was not designed to do...

As long as Perl does not have its own native GUI builder, I used workarounds.

Earlier I had a technique to use C++ Builder to design GUI and call Perl from C code (number of small scripts as shortcuts, embedded Perl and nothing more compilcated)

Now I use a technique of using VTCL and invoking it from Perl using Tcl::Tk module.
I described this earlier, please see it at A technique to create GUI design for Perl application using vtcl

I advice latter one as a way to go...

Courage, the Cowardly Dog