About the only thing you are doing wrong is over complicating your sample code. Consider:

#!/usr/bin/perl
use strict;
use warnings;

my $z = ~0;
printf "%b  0x%x  %d\n", $z, $z, $z;
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Prints:

1111111111111111111111111111111111111111111111111111111111111111  0xff
+ffffffffffffff  -1
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which is a 64 bit value with all bits set. That is the twos compliment representation of -1 and we've printed it as a binary value, a hex value and as a decimal value.

~ performs a bitwise compliment of the contents of a variable so the result is just what we expect. None of the subsequent operations you performed in your sample code changed the bit pattern.