Directory Setting Issues, i believe(kind of long)

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Apache 2.2.12 on SLES11 SP2. I have a couple of vhosts; the one i am concerned about is teknerds.conf. In teknerds.conf i have some rewrite rules (thanks Yehuda):
RewriteEngine On
RewriteRule ^/ifolder(.*) https://%{HTTP_HOST}/ifolder/ [L]
RewriteRule ^/admin(.*) https://%{HTTP_HOST}/admin/ [L]
to access some file services on the server (http://teknerds.net/ifolder).

I also have a install of OTRS (ticketing system) written in perl(http://teknerds.net/otrs/customer.pl). In order to make this easier for clients to get to, i have made otrs accessible by http://helpdesk.teknerds.net by doing this:

making a new vhost.conf called helpdesk.teknerds.conf and adding this to that vhost.conf:

DocumentRoot /opt/otrs/bin/cgi-bin/

and adding this to the otrs.conf file which is in /etc/apache2/conf.d:

# agent, admin and customer frontend
Alias /otrs-web/ "/opt/otrs/var/httpd/htdocs/"
Alias / "/opt/otrs/bin/cgi-bin/"

this use to be:

# agent, admin and customer frontend
ScriptAlias / "/opt/otrs/bin/cgi-bin/"
Alias /otrs-web/ "/opt/otrs/var/httpd/htdocs/"
notice it is flipped and "Script" is removed.

I also commented out the location otrs.conf:
# set mod_perl2 options
#    <Location /otrs>
#        ErrorDocument 403 /otrs/customer.pl
#        ErrorDocument 403 /otrs/index.pl
#        SetHandler  perl-script
#       PerlResponseHandler ModPerl::Registry
#        Options +ExecCGI
#        PerlOptions +ParseHeaders
#        PerlOptions +SetupEnv
#        Order allow,deny
#        Allow from all
#    </Location>
and then entered some of the commented out info from location otrs.conf into the otrs.conf directory:

# directory settings
<Directory "/opt/otrs/bin/cgi-bin/">
    AllowOverride None
    Options +ExecCGI -Includes
    Order allow,deny
    Allow from all
    ErrorDocument 403 /otrs/customer.pl
    DirectoryIndex customer.pl
    AddHandler perl-script .pl .cgi
    PerlResponseHandler ModPerl::Registry
    PerlOptions +ParseHeaders
</Directory>

Now, i can access http://helpdesk.teknerds.net and get the customer login page of the ticketing system like i want to. The problem is, i can no longer access http://teknerds.net/ifolder (and a few other http://teknerds.net/(whatever).
I know this is long but i wanted to give all the info i could and what exactly i did before the other stuff broke. How do i access the other http://xx.xxx/(whatevers) and http://helpdesk.xx.xxx?

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