My intuition on this is that OS X and its applications aren't designed to operate in multiple instances. When two processes are making changes to the same preference .plist files concurrently, you might get unintended behavior. Some applications are designed to work in a "project library" setup, like GarageBand and the new iMovie (these applications can only work on one project at a time), but if Xcode allows you to open multiple projects at the same time, that's definitely the way to go. Almost all document-based applications work this way, ex: Office, TextEdit, Safari.
If you're new to Mac, it will soon become apparent that a window is not the same thing as a running application. A single application may have many windows at a time, and closing all of those windows individually does not necessarily close the application (though this will occasionally be the case, see System Preferences.) Instead of switching between windows with alt-tab, you switch between applications with Command-Tab, and switch between that application's open windows with Command-` (tilde). When closing applications, get into the habit of choosing quit from the application menu (or hitting the near-universal Command-Q) instead of x-ing out of every open window. In most cases this will leave the application still running with 0 open windows. Running applications are denoted with a glowing light under their dock icons, and will also show up in the Command-Tab application switcher.
Protip: when closing down multiple applications quickly, hold down Command, use Tab or shift-Tab to select each application you want to close, and smack q to send each one a quit command.