how to tune ports in an enclosure?

Unless you know the exact cubic feet of space, it's going to be a trial and error effort. I'm sure there are ways to change the tunning such as, placing filler materials to take up space in the trunk. I've heard of crazy things like, rocks, bricks, blankets .. etc.

As far as the ports, you could just start sticking tubes from the deck down into the enclosure space just to see how that would affect the sound again, trial and error. The MOST concern here is protecting the subs from over excursion damage. I am not certain if those subs specs or if the space in your trunk is so large that the application is considered as an infinite baffle.

Typically subs are placed into an enclosure for tunning and to prevent the sub from bottoming out which could damage the sub. There are other reasons as well.  When a enclosure is designed specifically for a sub, those internal dimensions are taken into consideration and port tunning dimensions are easily calculated.

I am CERTAIN others will be glad to post more information about your application.

ok, I believe I misunderstood your application.

There is a "box" or enclosure. Not the trunk space as part of the internal dimensions of the enclosure.

You need to confirm internal volume of the box plus the displacement of the subs and bracing if any. Decide what frequency you want to tune and hopefully you have enough length to place proper lenght port to acheive that tunning frequency.