Sealed or Ported box?
 

I know it's not the ideal location for a sub enclosure but what is the best to put up under the passenger side helm area? Ported or sealed box with a JL 12

General concept (to my knowledge) is that a ported box will be louder, but a sealed box can be tuned.... if you just want loud, port.

Most JL Audio subs are medium 'Q' and will function effectively in either sealed or ported enclosures.
Sealed will give you a higher but more gradual low frequency roll-off.
Ported will give you about 1/3rd octave more deep bass extension before rolling off far more abruptly. In a ported SQ alignment you can expect a + 3 dB increase in the deep bass output.
So if you can afford the much larger enclosure displacement it makes sense to go for the extra output of ported, especially with the serious losses you will incur within the passenger side locker.

Normally I would choose the added output of ported, but if given a choice between direct-radiating and sealed on the driver's side versus concealed and ported on the passenger side, it's a no brainer. Sealed on the driver's side. No contest.

If you do go to the passenger side you should have a large vent equal to or larger than the woofer surface area to allow the bass energy to flow from the compartment. Otherwise, you will have nothing more than a tactile boat shaker and a very poor musical bass maker.

David, I ended up getting the JL AUDIO CP112-W0V3 4 ohm bass wedge. It will suit my needs for now. I'm pushing it with a wetsounds HT6 so that's 300 watts in a perfect world. What should I set my hrtz at for this particular box and sub. Not sure on gain either.

The correct selections are part of a sequential step-by-step tuning prescription. There is no single number that fits all.
For example, the upstream voltage of the source electronics will help determine the amplifier gain so that must be set first. Beyond that, the sub output must match the output of the coaxial satellites through a symmetrical crossover region. A direct radiating sub and a concealed sub (within port locker) will have different numbers.
At this point, anything that I or anyone else could give you is a completely arbitrary number.
I recommend that people go through Odin at Earmark Marine because he will walk you through the step by step process. Then you'll arrive at the correct settings for your boat and application.

Here is one area of caution. It is the upper bass that gives the audible clues for sub distortion. In a port locker those clues will be attenuated the most. So you could be over-working the sub amplifier and driver without knowing it, particularly when the boat is in motion. Based on that I think I would find my limitations with the sub/enclosure temporarily outside the locker. Then use that as the maximum guideline when the sub/enclosure is returned to the locker. Maybe this will give you enough bass output and maybe it won't but it will save you from placing the amplifier in thermal or toasting the sub driver.