You can probably safely ignore the manual from Neptune and use the Un-Official guide instead (although it wouldn't hurt to read both!). It's exteremely comprehensive and helps you through various setup options.
Personally, I've run a network cable to my basement then to my aquarium. That way I didn't have to mess around with the wireless configuration. Also, when upgrading firmware, etc, it's best that you hardwire it.
My network cable is a light beige colour so I've run it around the room against the floorboards and it blends in with the carpet.
Never had any real issues yet doing it this way.
Good luck! The hardest part is setting up port forwarding on your router and setting up DynDns.com so you can access it from outside of you home.
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