Having multiple monitors is great. You have a lot more desktop real estate to use. But there is one annoyance in Ubuntu that has irked me for a while. By default my Ubuntu installation treated both of my monitors as one large desktop. If I maximized a window, it would stretch across both screens. Finally I figured out how to prevent this. This method assumes you are using hardware accelleration along with Compiz, and Ubuntu is already set up for multiple monitors. Here are the steps:

1. Start the CompizConfig Settings Manager, which (if installed) can usually be found under System -> Preferences.
2. Under the "General" section, click on General Options. Go to the Display Settings tab.
3. Deselect the "Detect Outputs" option.
4. Under "Outputs", there will be one item listed, e.g. "2880x900+0+0". Select this item, and click Delete.
5. Click on New, then enter the resolution of your first (normally left most) monitor, followed by "+0+0". For example: "1280x800+0+0". Then click Close.
6. Click on New again, then enter the resolution of your second monitor, as above, but instead of the first 0, enter the horizontal resolution of the first monitor. For Example: "1600x900+1280+0". This tells the system where, in relation to the first monitor, the desktop space of the second monitor begins. Then click Close.
7. The setup should now be complete. When you open a window, it won't appear half-way on one screen and half-way on the other, and if you maximize, it will fill only the monitor it's currently on.