Hmm.. lets see where to start... ok number one.
1.) When you create a user account in Site Manager you ofcourse have the option to enable email and ftp. I think the email is pretty self explanitory and you seem to understand that. The ftp part means that like you they can use ftp to upload files to the directory you specified for them. It could be that you want them to use this as their own little mini site with in yours. So they could have an index.html page as thier home page and then others just like on your main site. When someone went to that directory thier site whould show up. Sometimes you may want to start out by enableing ftp for an account and then go right back in and disable it but leave the direcotory that was created. Folks do this so that then they can put a config file in for Spamassassin for that user that is different then the main one. It also seems to have this directory there even if it is not enabled for some other scripts that are used on your site.
Oh when you create a user in your site manager they end up haveing a little mini site manager of thier own. You can access it from yours by clicking on thier username. They can access it by going to http://yourdomain.com/users/
and logging in. yourdomain.com is replaced with your domain ofcourse.
3.) Kind of answered in one but if you wanted them to be private you could do that and there are alot of different ways. If you for sure want them to be public and viewable by others via a browser then make sure that users directory is in /var/www/html.
2.) To make a file downloadable you can nomally simply make the link to it in a url something like http://ftp://userdirecotry/somefile.ext
of course your path would be to where ever the file is and the file name would that of the file and the extension for it.
On the second site question. If you put the second site in /var/www/html then it is going to be viewable via a web browser by default. If you put it in /var/www then I think you would have to do some manual modification of the httpd.conf file that is found in /ect/httpd/conf/ in order for it to be viewable. I could be wrong about that but I think I am right.
By default anything that is in the /var/ww/html directory can be viewed by a browser. If you FTP into your site and then go to /var/www you should see three directories - cgi-bin, html and icons. If you then go to your html directory you'll notice that there is a symbolic link for the cgi-bin that actually leads back to the one you just saw in /var/www. There are alot of these symbolic links scattered about in other parts of account and they can be a bit confusing at times. On my FTP the icon used to display a symbolic link is kind of a half folder and half file image. Don't know if you FTP program does that or not.
I hope that answers some of you questions and that I did not get to involved. I sometimes over explain things.
Feel free to ask for clairification on any of it. There is much to learn and I still learn something new every day. Email is the hardest thing for me sometimes. If you have not checked out Jalal's site you might want to. There is a pretty good overview of how the mail system works and some good hints for manipulating it. The link is at the top of the main forum and in all his post at the WH forum.
I learn by trial and error lots of times. I have one account/site that I use just for trying things out. It is not a live site that folks use so I don't have to worry about making anyone mad.
Most the mistakes I make is something real simple or a typo in something I've uploaded... sometimes it helps to post what you are working on for others to look at so they can manybe catch something simple you have missed. I have tons of books that I keep close for refrence and I use Google pretty heavily. Searching can be hit and miss sometimes it just depends on if you can get the right combination of keywords. Well those are just a few pointers of how I get by don't know if they well help you any but thought I would pass them on.