On the assumption that every $cn will match at most one $bn (or that you don't care about more than the first), you could precompile a regex and use the result of the match:

#!/usr/bin/perl

use strict;
use warnings;

my @CS_CHECKS = ( '00012345', 'D123470', '0000123450', '0000023456', '
+50000123990' );
my @B_CHECKS = ( '1234', '12345', '123990', '12399' );

my $re = do { my $x = join '|', map "\Q$_", @B_CHECKS; qr/^[056]0+($x)
+$/ };

$_ =~ $re and print "$1 = $_\n" for @CS_CHECKS;
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Of course, the regex engine is still run through the alternatives (up until one matches), but at least it looks more elegant. :)

(Oh, and it may be faster too, what with not having to recompile the regex again and again. But don't quote me on that.)