I'll asumme that you have installed mod_perl (from RPMs, compiling), koha is running in /usr/local/koha and you have apache 2.0.49 (I'm under SuSE 9.1).

First in your mod_perl-startup.pl  change use lib qw( /usr/local/koha/intranet/modules ); to:
use lib qw(/srv/www/perl-lib /usr/local/koha/intranet/modules );

Now go to your http configuration and find where you  have the virtual servers. for each virtual server add something like this:

<Location /cgi-bin/koha/>
        # mod_perl mode
        SetHandler perl-script
        PerlResponseHandler ModPerl::Registry
        PerlOptions +ParseHeaders
        Options +ExecCGI
    </Location>


More or less this is my setup, this is not a howto, maybe someone can write something more detailed.