.htaccess configuration with wpmu

Hi

i have installed affiliate system and i cant access it cauz of .htaccess configuration, and need to know what to do:

I've just installed WPMU and it is inside a folder called (WP) but running from the root (public_html)

and here is the details inside :
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# add a trailing slash to /wp-admin
RewriteRule ^wp-admin$ wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^(wp-(content|admin|includes).*) wp/$1 [L]
RewriteRule ^(.*\.php)$ wp/$1 [L]
RewriteRule . index.php [L]

****************************

I've installed JROX Affiliate manager in a folder (affiliates)

and when i run it i get wrong address and it shows the wordpress as i called a wrong address

the Affiliates Folder .htaccess has this inside:
DirectoryIndex index.php
#Options -Indexes

<ifModule mod_rewrite.c>
RewriteEngine On

# Some accounts require the RewriteBase to be set
#RewriteBase /

# Rewrite rule for replicated webpages
# RewriteRule ^r/(.+)$ jrox.php?rep=$1

RewriteCond %{REQUEST_URI} ^/system.*
RewriteRule ^(.*)$ index.php?/$1 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.+)$ index.php?/$1 [L]
</ifModule>

<ifModule mod_deflate.c>
# compress text, html, javascript, css, xml:
AddOutputFilterByType DEFLATE text/plain
AddOutputFilterByType DEFLATE text/html
AddOutputFilterByType DEFLATE text/xml
AddOutputFilterByType DEFLATE text/css
AddOutputFilterByType DEFLATE application/xml
AddOutputFilterByType DEFLATE application/xhtml+xml
AddOutputFilterByType DEFLATE application/rss+xml
AddOutputFilterByType DEFLATE application/javascript
AddOutputFilterByType DEFLATE application/x-javascript

# Or, compress certain file types by extension:

<filesMatch "\.(js|css|html)$">
SetOutputFilter DEFLATE
</filesMatch>
</IfModule>

<IfModule mod_expires.c>
# Activate mod_expires for this directory
ExpiresActive on

# locally cache common image types for 7 days
ExpiresByType image/x-icon "access plus 2592000 seconds"
ExpiresByType image/jpeg "access plus 2592000 seconds"
ExpiresByType image/png "access plus 2592000 seconds"
ExpiresByType image/gif "access plus 2592000 seconds"

# cache CSS files for 24 hours
ExpiresByType text/css "access plus 24 hours"
</IfModule>
***************************************

So what do i have to do?