Hi tschmid4,
You can have a .htaccess file in every directory. I can’t say I understand the structure of your site, but the ones that are present already are used by Akismet. You can simply leave these where they are.
To enable multisite you need to make a change to the .htaccess file in the root of your WordPress installation. That is where you also find your wp-config.php, as well as the folders wp-admin, wp-content and wp-includes.
If there is no .htaccess in your root, you probably did not enable pretty permalinks yet. This is recommended.
If you did, or you can’t and you still do not have an .htaccess file you can create one yourself with the following content. This is for a single installation:
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
In case you have trouble creating such file (without a filename) you can give it a name, f.ex. a.htaccess, and rename after you upload it through FTP.
When you activate multisite WordPress will present you with new content for this .htaccess file. You can paste this between # BEGIN WordPress and #END WordPress.
More information about this can be found in the Codex and here is a good read for a more in depth introduction to .htaccess. Beware though, not everything written there will suite your install. Always keep a backup when you replace this file.
I hope this helps. GL with it!