ssh is only the means to access your server; in fact, you're asking for help with shell commands.
Go with midnight commander for now, will get you started nicely. If you're connecting your server to the internet as a web server you will save yourself a lot of time and grief by getting it hardened by platinum servers or one of the other companies providing that service.
BTW unix commands are always typed in lower case, both to the shell and to forums like this.
I think Khunj and Brianoz are correct in what they are trying to say to you, but allow me to reiterate, of your not comfortable with SSH you may wish to practice on something that isn't a production environment, try www.cygwin.com, it's a Linux-like shell environment for Windows what will let you get some experience.
On that same note, to help you with your current problem you may not want to jump into installing programs, is there a hosting control panel installed on the server like Plesk or Cpanel, they normally have a web file manager included that can alter file ownerships and permissions?
Having a bit of trouble when ssh'ing into a server I didn't set up, ive not been that confident with SSH (yes its powerful, but also unforgiving).
I think the only way im going to be able to CHOWN the folders i need is through the root login.
When I do this however it logs in fine, but then i type LS and it comes back about creating 3 certificate files.
Can anyone give me a quick rundown how how I will navigate to the html folders to change the owners of the folders I need?
There are 2 domains on this single Plesk ran server.
Using Putty if thats of any use.
You might also check to see if Plesk offers a simple file browser/editor utility.
If learning is where you want to go with this, I would download VMware Server (free) and load a copy of the same Linux distribution you are using. This will allow you to get the feel of the operating system without affecting a "production" system.
=> • Admo.net Managed Hosting • => Managed Hosting • Dedicated Servers • Colocation => Dark Fiber Access to 1102 Grand, Multiple Public Providers => Over •Sixteen• Years of Service