I will answer these questions as you asked them.
Quote:
| How can I upload file to a VPS |
If you have a control panel installed such as ravencore, directadmin, or cpanel - just by creating a account will allow you ftp access to upload files. If you do not have a control panel, you can use winscp as a sftp client to log into your server as a file system.
Quote:
| How can I run some apliccations |
Depends. As you said you want to admin and manage a linux based vps, you will have to run linux applications only. I've tested out wine (windows plugin) and ran a few windows applications, but they did not work as well as they worked on windows itself (go figure

). Reading a manual to the applications usually tells you what command to start it. Most of them are in the liking of,
./setup.sh
./install
sh install
And so on.
Quote:
| How to host a site in a VPS |
With a control panel it's very easy, without, you need to install dns servers, setup each record accordingly, add the dns in your registar (you have to do this part anyways), and create apache directory. It's optional to install ftp as you can just use winscp to update your files. It works almost the same.
Thanks!