First off, welcome to the world of Ubuntu!
Okay, when I first started using Ubuntu, a few years back, I was completely blank. I had no idea how to install applications in it, nor did I understand anything in the command line; heck, I didn't even know how to install Ubuntu! So I stumbled upon the (very well written, in my opinion) Ubuntu Pocket Guide which can be downloaded for free here. This guide walks you through almost everything a beginner can wish for, from installing Ubuntu (on its own, or alongside Windows), to understanding command line, to understanding the Linux file structure. Even though the guide seems a bit huge (170 pages as of now), it really helped me out in a lot of ways. I occasionally find myself resorting to it sometimes. I'm no professional in Linux, but everything I know now started from this guide, so I highly advice reading it. If you don't want to read the whole guide, read the chapters that you want to know about more.
Another very useful link is this. It gives an overview of the command line, and is also a good place to start if you want to learn a bit about the terminal.
Unfortunately, I do not know of any application that will help you understand command line, but the above should be sufficient for a beginner.