Beny:
It seems like your first real step is to start by putting together some diagram of some sort to describe exactly what you will be intending to build. From your posting it appears that you are somewhat unsure about connectivity and just how "features" should work. A detailed drawing can help to sort out this stuff. Work from the outside design first and then drill down to implementation details layer by layer as you learn just what is needed and how it would be achieved.

Trying to get your arms around what to do by looking at cut and paste stuff at web sites will not be the best way to get anything done. It will frustrate you at each turn and seriously impede the learning process.

You will also do well to read everything you can about the MCU of your choice. Learn about how it works and what it can do. Then you will have a much better understanding of how to apply it to implementing the functions that you desire to achieve as documented in your drawing.

Let me comment about the multiple alarm thing you asked about. If it is your intent that each alarm function would activate a separate annunciator (whether that be a light, noise maker or shocking device) then you will need a separate output pin for each. On the other hand if it is desired to use the same annunciator for all of the logical alarm functions then is sufficient to have just one output to activate the device.

Michael Karas