How To Keep Your Apps Organized In The Right Desktop Using Mac OSX Lion, Mission Control

"In Mission Control, apps are assigned to different desktops without my control, and these desktops seem constantly reordered."

You can manage this with Mission control. 

1. Go to System Prefs/Mission Control

2. Uncheck "Automatically rearrange spaces based on most recent use"

3. Open an app in the preferred desktop

4. Right click its icon in the dock

5. Select Options/Assign to Current Desktop

 
Now, when you restart your Mac, your apps will be on the right desktops you chose.