"The port I assumed would be "square" 4" wide, 12" length/vertical..."

so... 4" wide, 12" tall, and 12" deep? thats .33 cu. ft. of space. in a 3.2 cu. ft. (net) box, your tuning is going to be around 45-50hz. thats getting a bit high. use a round port (aeroports are great) that is 4" in diameter and around 12" long. it reduces your port crossection by 75%, but its still plenty of area to eleminate any port noise, and will drop your tuning into the low 30hz range.

to contridict the above statement, the best box i could possibly build for my AW1500s was 4 cu. ft. per sub ported and tuned to 35hz. of course, that was in a wall, lol. however...i still dont think you will make the space to fit both subs and the enclosure you desire. if you are new to box building i would recommend you go the sealed route first.

one more thing: it DOES matter where your ports are. put them on the same plane as the subs and around 1/2 the diameter of the sub away (so for a 12" sub, you want them around 6" away, although anything close to that is fine. the phasic interaction will be nearly identical as long as its on the same plane). also, never ever ever fire your subs forward (toward the engine side, lol) in an eclipse unless you have a static barier to eliminate cancellation due to wave reflection/interaction (i.e. a wall). ive found that rear firing or up firing are the best ways to go.