can you install themes with this program?
The very short answer to your question is yes...you can install themes via SSH.
You are obviously trying to learn your iPhone better. Let me clarify some things if they haven't been already.
The Cydia app "SSH" is a package that allows you to remotely Terminal access your iPhone through its IP address. "SSH" installs itself as a Service that runs in the background on the phone.
The Cydia app "MobileTerminal" is an App that provides you local access to your iPhone. (Same access as SSH...just locally done instead of remotely.)
Two user accounts are on the iPhone by default. These are "root" and "mobile", and both have the password "alpine". SSH will ask you for a username and password. MobileTerminal will automatically log you in as "mobile" for you.
(Note: Because the "root" and "mobile" passwords of "alpine" are well known, you need to change them right away to something else if you haven't already. Use either SSH or use MobileTerminal to get into the phone. There are multiple tutorials on the internet telling you how to use the "passwd" program to change passwords.)
Once you access your iPhone through SSH or MobileTerminal, you will be placed into a text-based CLI or "command line interface". The name of the CLI is "bash". (You can find this by typing "sh --version" at the command prompt.
When logged in as "root" at the CLI, you should have unrestricted access to you phone. You can rename files, delete whole directories at time, change the files owner, etc, etc. I highly recommend you google "basic linux commands" to learn more. (For example:
http://www.reallylinux.com/docs/basic.shtml looks like a good start.)
You can do great damage to your phone (up to the point of possibly bricking it) so be very careful what you type. When in doubt, look up the command on google (or similar) before typing it. Once you get good at the CLI, you'll be able to do cool things like directly install beta software, and modify Winterboard themes at will (or make your own).
Terms for you to google/research:
"basic linux commands"
"bash"
"apt-get"
"dpkg"
One other thing... I encourage you to install SBSettings if you haven't already. SBSettings as a "SSH Toggle" so you can shut down the background SSH process when you aren't using it.