Hi Surge1243,
The spacers (or stand-offs) are used between the motherboard and the mounting plate. Without them, the motherboard will make contact with the mounting plate (something you don't want it to do), this will cause an electrical short and your system won't work.
To use/install the stand-offs, you hold your motherboard over the mounting plate and see which holes match up to the mounting plate screw holes. Install the stand-offs in the holes you determined to match the motherboard holes. Then you lay the motherboard on the stand-offs and screw the board to them using the screws provided. You should match as many mounting holes to the motherboard as you can so the board is well supported. This prevents the motherboard from bending too much when you install your cards, cables, wires, etc...
Since this is your first build, my suggestion is to take everything apart and then take the time to read the "Build Your Own PC" section of this website. It's very well written, has explanations of parts and terminology and will walk you though each step :
http://www.pcmech.com/byopc/index.htm
Cricket