It sounds like you are off to a good start, research!
The 125 is what is called a "reef ready" tank. It means that it is pre-drilled in order to have a sump under the tank. One of each of those holes is for a drain to the sump, the other hole is for a return to the tank.
Are the hold surrounded by plastic with little fingers at the top to strain the water?
Depending on how good you are with DIY and how much research you want to do, making things your self is very rewarding along with a lot cheaper. If you have money then you can always go with pre-made. You can always go to your local fish store and see what they have available but remember that it is usually their objective to sell to you, so research before you buy.
Lastly, look up information on fishless cycling.