Im not convinced that what you are doing is the correct way to your goal (which I am unsure exactly what that is).

I would have code handle all arguments via initial command line, then branch out depending on what needed to be done. If you needed to call a new module or script, do it via code, not via the command line.

Here is my crappy (super duper crappy wappy) possibility to your probable goal :

use strict;

my $a_a_switch_param;
my $a_b_switch_param;
my $c_b_switch_param;
my $b_a_switch_param;
my $b_b_switch_param;

for (my $argcnt=0;$argcnt<=$#ARGV;$argcnt++) {
     my $arg=$ARGV[$argcnt];
     if($arg eq "-a") {
         $argcnt++;
         $a_a_switch_param=$ARGV[$argcnt];
     }elsif($arg eq "-b") {
         $argcnt++;
         $a_b_switch_param=$ARGV[$argcnt];
     }elsif($arg eq "-c") {
         $argcnt++;
         $a_c_switch_param=$ARGV[$argcnt];
     }elsif($arg eq "-ba") {
         $argcnt++;
         $b_a_switch_param=$ARGV[$argcnt];
     }elsif($arg eq "-bb") {
         $argcnt++;
         $b_b_switch_param=$ARGV[$argcnt];
     }
}

my $b_prog_output=qx/perl b.pl $b_a_switch_param $b_b_switch_param/;
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