From there, you choose your data drive for the first instance, and the installation begins. To install the second partition, go through setup again, and it will recognize the initial partition and ask you for information about the data and name for the second partition.
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Once you are installed, all you have to do is change the notes.ini settings (which are now in each respective data directory) to point to the correct IP addresses. You can find all of the setting changes you need in the Administration Help database.
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