honestly, im not quite sure what ported means. ive just never seen people intentionally putting the subs face down. Struck me as odd.. and what do you mean by "you get the sound of the back side of the speaker"?
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Ported means the air can escape from the box. there will be large holes in the box, usually with some pvc tube mounted in them. The Thump you hear is from the speaker compressing air in the box. The theroy is you woull get more sound if the back of the speaker is up. Also it hits the vehicle floor and makes more noise.
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The main reason you want to face the subs down is so the output is pushed out from under the seat instead of into it. This is the compression factor NGM mentioned. You do this with cars and SUVs as well. In most vehicles you face the subs toward the back. Some vehicles will sound better with the sub facing up or left/right. It just depends on the vehicle as to what sounds best. There aren't really a lot of options in a truck.
facing down makes basicaly makes the sound waves "bounce" to a certain extint. where going into the seat they will somewhat muffled especially if you have a sealed box. If you have the chance and have a store in your area that has the mtx thunderforms try and listen to one of them and see what you think.. there is also another company out there that makes boxes like this but i cant think of the name of them off hand. pretty much the way ngm stated above.
Suggest that another factor is that low frequencies are not as directional as the higher ones.
As long as the 'sub' can disturb some air, it doesn't make as great a difference as to which direction its pointed. A greater portion of their effect is felt, and not so much heard as compared to the mids and tweets.
On the other hand, the tweeters are usually located so to be a direct 'line-of-sight' to the ears, or reflected off a hard surface such as a windshield.