I am new to Unity and am wondering how to use the actual programming part of the engine? I have used Microsoft Visual Studio and used it to create sprites when I was taking a beginning programming class. I have looked at tutorials using unity but am still very confused. Any answers would be very appreciated for a new user/beginner programmer. Thanks.
Just to follow on from what has already been said, the Unity Script References are also very useful to read through and see some basic scripting examples.
http://docs.unity3d.com/Documentation/ScriptReference/index.html
Right click on the project view, create > C# script or Javascript. Double click or press enter while highlighting the script to open it up. Monodevelop will open the script.
One thing to note, if you use C#, the script name must be the same as the class name or else the script wont work. It automatically does this when you first create a script. If you want to change your IDE to Visual Studio, follow this link: How to set Visual Studio 2010 as default script editor in Unity - Unity Answers
Good luck
A really good book for learning C# is “Learning C# by Developing Games with Unity 3D Beginner’s Guide”. It goes over the basics you need to know in order to start programming. Once you have read that book you should have a good understanding of the language.
You can get the book from here: Search | Packt Subscription
If you’re familiar with Visual Studio, then keep using that, as it is by far the most powerful coding IDE, especially with Resharper installed. There is also a third party tool called UnityVS which allows you to debug your Unity code in VS.