Check the Rough Opening

At this point, try and get a good idea for the condition of the opening. Use a 2' level to check the sides and the sill. If it looks pretty good, in most cases it will, you're ready to install your first window. If it's real bad out, you can shim it.
Here again, the type of window you select will determine exactly how it is installed. Some will be flushed with the inside, some with the outside, some in the middle. Wooden windows might require predrilling holes and Vinyl Windows will usually have holes already predrilled. Discuss these topics with your Window Rep to decide how you will be finishing the window out. You might want, for example, to install wooden jam extensions on the inside to beautify the window. If you are looking for easy installation and low maintenance, your window rep can get windows that will closely match the size characteristics of your existing windows, making it a simple task to remove the old windows and replace them with the New Windows.

Plumb, Level, and Square

Whatever method you're using, be sure to install the window plumb, level, and square. I usually position the window in the opening and put a screw in an upper corner. If you checked the opening out before this, you'll know which side, if any, is high. Screw on the high side, since you can easily raise the low side. Use a tape measure to set the window in the correct depth at each corner. Use a 2' level to get the window plumb in both direction. Place a screw on the opposite side and then check to see if it is square. To do this, measure diagonally from each corner. Top left, to bottom right. Then Top right, to bottom left. They should be the same, if they are, the window is in square. Go ahead and screw in the bottom corners, being careful not to over tighten them. Then re-check for square, level, and plumb. If the window is not square, you'll have to remove a screw and try to tweak it a bit. You can also use wooden shims at the corners and in the middle. Don't jam shims in though, as that can warp the window and keep it from operating smoothly.

Insulating Your New Window

You will likely have a gap around the window, between the window frame and the rough opening. You want to fill this with insulation. I do not like to use the expanding foam type for this, as it can put pressure on the window, and it is messy to clean up. Instead, use regular insulation. Depending on how many windows you have to do, you can probably find a small roll. Pull it off the paper backing and use your pry bar to lightly slide it into the gap. You want it to go from the outside to the inside, but do no over pack it. This to can cause warping and hinder window operation.

Go all around the window and check for gaps. Feel for wind blowing. Look for daylight. If the gap is ¼" or smaller, you'll probably just use caulk to seal it, because stuffing insulation in there can be difficult.

Buttoning Up

Follow the manufacturers recommendation for quantity and locations of screws. Some windows come with screws, some don't. You want to make good contact with the framing to keep the window from moving, but don't over tighten screws. I like to check the window operation at various stages of the installation to make sure it still opens and closes smoothly.

When the window is secure and operates properly, go outside and caulk any gaps with silicon or an approved window caulk. All that is left is finishing the inside and outside with trim. A popular outside treatment is metal Deluxing where you wrap the old trim with painted metal. There are separate articles on this site for finishing the inside and outside of your windows. You can install all your windows first, and then go back and finish them out. Just be sure any window is water proof before moving on, incase you get caught in foul weather.