I am installing a Lowrance HDS 12 PRO on the bow of my boat, but the wiring harness included is only like 6 feet long so I am gonna have to run some duplex wire from the battery compartment to the bow and I am wondering what gauge I should use? Should I match the gauge of the included harness? Or upsize it since I will be running a longer length? 
 

I found some  “wiring kits” that have the duplex cable and fuse box and those use 10 gauge, but that seems overkill since the stock harness is around 18 gauge. Plus it’s much cheaper to just buy some duplex cable and get the fuse holder and terminals from my work. 
 

Also, does it matter if I run a plug setup like my trolling motor so I have a neat/water tight pass through? Or should I just run the wires straight through the deck/gunnel so I have fewer connection points and less chance for interference or whatever? 

When I ran mine I went a little overboard but I run alot on it.  If I was running 1 graph I'd run 10 ga marine wire.  If you go to small you can run into power issues. 

Check your manual or the Internet to see how many amps your unit pulls.   Measure the length of wire you will be running to the battery and double it to account for the wire from the battery to the unit and back.   Take these numbers and use a wire gauge chart like the one below to determine the size wire you need.   The smaller your wire the more voltage drop you will have.  Personally I would go with the 3% voltage drop number.  It’s also good to have a little extra capacity to accommodate your next big upgrade.
 

http://assets.***.com/files/resources/newsletter/images/DC_wire_selection_chartlg.jpg

Is there any reason not to use a Plug & Receptacle like the one below? I feel like it is a cleaner pass through of the deck/gunnel rather than just using a grommet. It uses 8ga wire so I don’t see it adding much resistance. 
 

I run everything direct to reduce failure points but its really a preference.