Understanding Virtual/Web min differences

Obviously, I am not a strong Linux type person. We have a current system under Ubuntu 10 LTS, which runs Webmin, and I have used that to create a couple of small virtual webservers. Things seem to be working fine, with the installs created in var/www/html for the base server, and then other folders in var/www/htmlserverA, var/www/htmlserverB etc.

We are in the process of changing over to a new ISP, with a fresh install of the Ubuntu 10 LTS software.

The first thing installed was webmin, the next item was virtualmin... and then a few users and some database tables. I used Webmin to create the same websites as noted above, and it seems that each of the extra sites now access the main html rather than their own. I'm going to guess, that's because Virtualmin is now running.

I guess I can toast them... but I like the ability of having them all under the var/www side, just for the sake of familiarity. Can this be done?

One of the other reasons I put in Virtualmin was to be able to setup a proper ftp type account. We have one custom windows-type desktop application, that we want to be able to allow the software to upload some pdf files into a specific folder, where those files can be accessed via ftp for generic "public type" download. The issue is, this app connects in to the database server based on the IP of the system, not based on a domain name. And I had huge issues with trying to create an ftp account/password, that had a restricted shell type definition, that would allow the uploads to take place. I believe our default ftp package is the ProFtpd thing. (sorry, I'm really a noobie... but I am trying to understand!) By the way, this custom app works just fine in accessing the database, which is used to store a description of the file, and a "link" to the file name.

Part of the issue is of course, using sftp, because I don't want the user name and password for the ftp connection to be passed un-encrypted.

Would I be better off nuking the existing Webmin virtual server definitions (leaving the .. I think ... default 2 entries in place) and then setting things up with the 'default' Virtualmin settings of creating and putting things into a new "home" directory? And if I do that... then would not "that" user account have access (ftp wise) to the entire html folder contents? Right at the moment, we are trying to use a separate folder in the base system html side, and set the owner of that to a different user name, trying to isolate them away from the rest of the website files.

Again, this particular application does NOT have a domain associated with it. So, I am kind of stuck on what's the best and proper course of action.

Advice is deeply appreciated! Thanks kindly in advance. :)