You can see a great instruction sequence on hanging molding at House of Hepworths here (which I found after we hung all of our boxes - darn it) or follow Sarah at Thrifty Decor here (with videos).
Here are my top three tips for beautiful boxes:
1. Make sure you make the baseboards level with the earth (not level with your floor). This will be invaluable when you are installing everything else. Use a level and make sure the bubble is in the center and then nail those puppies up. You may end up with a small gap under the baseboard, but its better than your whole wall looking crooked. It goes without saying perhaps that starting at the highest point on the floor is a good idea here.
2. Install the baseboard first, then the chair rail, then the boxes. This gives you a good reference point and will make your install WAY easier. Once the baseboards are level you can use your template and that molding will go up like gangbusters.
3. Cut and install the bottom of the box last. This piece is the one that you will notice the least (versus the top and sides), if you have any slight miscalculations in cutting you can hide them by cutting this piece slightly longer or shorter than the top so that you get a perfect fit.
Happy cutting and nailing! Oh and just a quick shout out to me because I used a nail gun for the first time and no one died... or bled. My husband MAY keep all power tools away from me because I tend to be