This should be possible using the SetEnv directive. Try putting this in your .htaccess:
SetEnv PERL5LIB /home/username/perl
If you want to add several paths, divide them into : for example:
SetEnv PERL5LIB /home/username/perl:/some/other/path
You can (of course) also use this to set other environment variables.
Another option is to add it to the include path from Perl itself. You will need to add the line use lib "/home/username/perl"; in the CGI script (s), somewhere, before loading the modules (modules) installed there.
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