klasrules

I got it to work, but I think it is a DNS and webserver config problem also.

I got al our domains directed to one main domain (directory). I think it is a Apache Serveralias configuration, I do not know, as it is a cpanel configuration I got on Loopia server provider.

I just went through the steps (also described here above):
1. Made a new website
2. Changed to the domain (root)
3. Moved it to main Network
4. Set a site as start page
5. Reloaded the Network.

You should have a .htaccess file in your root directory.

I d not know if the plugin create extra htaccess files, but its not any thing you need to bother with.

You can read here witch configuration you should have:

https://codex.www.ads-software.com/Multisite_Network_Administration

For an example, I got my websites and domains pointed to SubFolders (actually root for the domains = /):

RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ – [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).*) $2 [L]
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteRule . index.php [L]

Uncheck the box next to jQuery Extrem Protection (checked = yes).