I haven't fully evaluated or tested your code, but a couple of comments and, if I understood correctly, the answer to your question:

• For longer regexes, next to /x as you're already doing, I strongly recommend using different delimiters and especially named capture groups (perlre) and %+, as in:

  my $regex = qr{
          (?<foo> fo+ )
      }msx;
  "barfooobar" =~ $regex;
  print "<",$+{foo},">\n";     # prints "<fooo>"
  [download]

• In the regex you showed, if the overall regex matches, then ([@%\$]?) and ([\d]*) will not return undef but the empty string "", because those capture groups will always match at least () (that is, the empty string "").
• Your expressions like if( defined ($sigil = $1) eq "" ) don't make much sense to me, because you're testing the return value of defined, a boolean value, against the empty string. If you just want to check for definedness, then write if( defined($sigil = $1) ), and if you want the assignment to $sigil to happen only if $1 is defined, then write if( defined $1 ) { $sigil = $1; ...
• You might be interested in my module Config::Perl ;-)

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