A 3/4-inch gap off the deck won't cut it. That will change the driver's 'Q', accelerate the air speed and choke down the woofer's output. If the downfiring woofer exhausts in an omnidirectional pattern then you can get by with a little less than would be necessary when forcing the woofer's output through a confined and directional path. I would elevate the surround of a 12-inch woofer 2 1/2-inches off the sole. Make sure that you maintain a woofer exhaust path that is no less than the collective surface area of both drivers.
Since you don't have the width to position the woofers side-by-side I'm assuming that one woofer would be mounted behind the other. This means that the rear-mounted woofer is more loaded than the front woofer which is bad when both share the same enclosure. The forces exerted on the two woofers are different not to mention the different force applied to the enclosure internal air mass. Also, the rear woofer would serve to load the front woofer via the exhaust path.
You might narrow the enclosure width in order to side fire both woofers to opposite sides with a 2 1/2-inch minimum gap per each side. This provides a more symmetrical loading and places both drivers in identical distance, phase and pressure in respect to the port.
When you place two drivers and a port within a helm console structure you're loading into a more rigid air mass versus open air. This will mis-align the bass reflex tuning somewhat and may raise the tuning frequency. I would add 5 to 10% port length to offset this. While tuning a bit higher can be advantageous for more output in a boat, I'm more concerned with the unloading effect below the tuning frequency. Along these same lines I would definitely add a 30Hz subsonic filter to protect your woofers in this type of loading scenario. Versus a car, you shouldn't detect an audible difference in a towboat but its cheap insurance for any bass-reflex system.