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I need to edit different parts of the document side by side. I cannot split the editor into two parts. I tried to run another instance of it, but it just goes back to the same existing one. I'm using TexMakerX

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For example in emacs it is possible what you want. I guess starting different instances of TeXMakerX depends on your operating system. You may also have a look on diff tools like meld. –  student May 6 '12 at 19:14

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TexMakerX is now called TeXstudio, maybe you want to update to the newest version. TeXstudio supports multiple instances, you just need to launch it from the command line using the command line option --start-always.
More options are described in the user manual, section 4.10

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