The stud is called the "standoff". This gets screwed into the motherboard tray at the 9 screw holes before you put the motherboard in.
After that, you have to secure the I/O shield, the place of metal with cutouts for the back of the case, if it's not already secured.
Then you position the motherboard into the case and screw it in with screws. Make sure to have a washer in the screw so it acts like a padding (between the two as you stated).
Before you do all that, I would recommend you put the processor in and attach the heatsink.
Since this is your first time, I would HIGHLY
recommend you read some guides throughly, like this one: Assemble PC - Put everything together
***READ THIS: LOTS OF PICTURES: How To Assemble A PC By Hand
More to read: How To Assemble And Build A PC
Also, if you have any problems what so ever, put the parts down and post a thread. Wait until you have a good idea of what to do then proceed. Overall, the process is really simple.