I don't know if there is an official way of doing this but you can keep your modifications in your own files without changing those you got from CPAN.

use FindBin qw/ $Bin /;
use lib $Bin;

use CPAN::Module;
use MyPatches::CPAN::Module; # must comes second
[download]

If you have warnings turned on, you will be notified when a second sub replaces the first.