Basically (and these section nums are not related to your qns nums)
1. use Ubuntu's repositories and pkg mgr to install apache (& mysql if reqd).
Do not try to handbuild.
2. use vitrual hosts to separate each website
3. use htaccess ctrls, but put them in the vhost directory tags, not as .htaccess files in website dirs.
4. ensure only you are uploading content/pages etc. This may run into a lot of work later, but its best to start that way.
5. ensure only your user is in same group as apache (it may actually install as httpd user)
6. Edit /etc/ssh/sshd_config to only allow you to ssh in.
you should probably use ssh-auth-keys instead of a passwd, especially if you want to automate uploads/downloads.
You can also restrict by username, host etc etc http://www.openbsd.org/cgi-bin/man.c...nfig&sektion=5
There are a lot of HOWTOs on the net; try to find one that's specific to your distro+vesrion and get an LTS (Long Term Support) version of Ubuntu for this.
you should have no probs using filezilla or putty on the same lan.