Thanks Ken. That helped me do what I needed to do. Here's some code I used to test it, for anyone searching on the same problem.
#!/usr/bin/perl
use Getopt::Long;
GetOptions(\%opts,'foo','bar','tim');
map { ${"opt_$_"} = $opts{$_} } keys %opts;
@mainOptions=qw(foo bar tim);
map { do {$numOfMain++; $mainOption=$_;} if $opts{$_} } @mainOptions;
print "foohash=$opts{foo}\n";
print "opt_foo=$opt_foo\n";
print "barhash=$opts{bar}\n";
print "opt_bar=$opt_bar\n";
print "timhash=$opts{tim}\n";
print "opt_tim=$opt_tim\n";
print "numOfMain=$numOfMain\n";
print "mainOption=$mainOption\n";
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