When you first run the file that you download it will ask where you want to install the EQ2MAP updater, which by default will be some kind of Program Files\EQ2MAP Updater. You can let it install there or in Program Files x86\EQ2MAP fine.
Once you finish installing the updater and run it it should detect your EQ2 install and update your maps then. The location that you install the updater itself is completely separate from where EQ2 is installed.
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