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What do you mean by "go away"? If you mean removed from your hard drive, then no. If you mean it doesn't load automatically anymore, then yes. Also I assumed before that you have already configured your box to load up in runlevel 3. If not you can google or search this forum to figure that one out.
The .xinitrc file goes in ~ (an alias for your home directory). For me, ~ translates to /home/mike. Try going cd ~ and note that you'll end up in your home dir.