We're running it on a vm server as well. The server is in the same network as the clients, so there is no real need for a firewall between them (we simply don't scan the clients from outside at the moment). The scanning user is an AD account without access to anything and has been added to the administrators group on each client (via GPO).
The Lansweeper-server also hosts the package-share for most of these locations, only some have their own shares on one of their local servers because the line between us and them isn't that great (China and the US for example). All users have full access to the share, to make sure noone finds and deletes any content, it's hidden with $. If someone still manages to delete/change something then A) we have a history of the folder changes so we can go after them and rip their head of and B) We have daily backups of the whole server so we can restore it within 5 minutes.
The deployment jobs use the scanning user, it's already a local admin on each client and the packageshare is public anyways so no need for an additional user there.
So far this setup has been more than successfull. It's working almost too well so my boss now expects all updates to be installed on about 90% of the environment within 2 weeks. This basically means I have only 2 weeks to organise every last one of our ~1500 clients (randomly distributed worldwide)