Multisite installed under standard WP install

Hopefully Mika Epstein or Andrea Rennick can add their .2 cents as well.

I am running 3 WP setups under a single domain.

http://www.DomainName.com/ (standard WP)
http://www.DomainName.com/members/ (standard WP)
http://www.DomainName.com/salesfunnels/ (multisite – sub dir, No domain map)
http://www.DomainName.com/salesfunnels/ (my network sites)

The problem I am having is my network sites, home page shows up but without a theme and wp-admin can not be found, i.e., http://www.DomainName.com/salesfunnels/test-site/wp-admin.

Right now I do not have domain mapping setup.

When you view the sites under the Network menu, the primary or root site is:

/salesfunnels/ as opposed to ‘/’ if Multisite was installed in the domain root as opposed to the /salesfunnles/ directory.

The network sites show as:

/salesfunnels/

I have never installed Multisite under a sub directory. Do I need to do somehting different or is it just not advisable?

/***********/

Before I setup Multisite my .htaccess file had the basic WP stuff in it and of course Multisite gave me more line to add.

My question…there is redundancy in the two but the redundancy is wrapped in <IfModule mod_rewrite.c></IfModule/>…do I jsut add the new lines under the old or add them under it.

Also is it possible the .htaccess file is the problem behind me network site issue?

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /salesfunnels/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /salesfunnels/index.php [L]
</IfModule>

# END WordPress

RewriteEngine On
RewriteBase /salesfunnels/
RewriteRule ^index\.php$ - [L]

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule  ^[_0-9a-zA-Z-]+/(wp-(content|admin|includes).*) $1 [L]
RewriteRule  ^[_0-9a-zA-Z-]+/(.*\.php)$ $1 [L]
RewriteRule . index.php [L]