SPL is not going to be affected by length enough to notice, signal however, has more chance to be interfered over greater distances, but once again, remedied by a proper install.
Some things that need to be noted about both trunk installs and underseat installs.
Underseat installs:
There are a few positives to this setup.
One of them is that your wires are much shorter to run between head unit to amp, and also from engine bay to amp. This makes wiring a bit cheaper, and easier due to the fact that you are ripping up far less materials to hide your
installation wires.
You also have the advantage of being able to adjust your setting easily without getting out of your car, if installed in a position that allows easy access to the amplifier controls.
Another advantage is that you have the added cooling of your internal cabin during hot summer months. I usually run the AC at body and feet during the summer, so it would run over the top of my amp and carry away heat while cooling the heatsink surface down.
A disadvantage of installing it under the seat is the problem of space. Often times an amp is too long or too tall, making the install impossible. If the amp is too tall, it could actually reduce free moving air and build up heat, throwing the amp into thermal protection.
Another disadvantage is cost of materials to protect the amp. This all depends on what materials you use, or even if you bother. The reason for building something around the amp under a seat is to protect it from people kicking your amp, or items slipping under there and causing heat build up.
And lastly is securely mounting under a seat. Some people like to use velcro, some screws. In a better situation, it is wise to modify a piece of generic steel and use a bolt to secure the metal in place, and use that as a mounting bracket. Either way, it is more headache and a few more bucks.
Trunk Installs:
Trunk installs are the majority of audio installs (in cars). This is due to having a good amount of room to use.
Some advantages of trunk installs are:
Ease of mounting and out of sight. You can generally mount your amp into anything at the back, if done correctly. One thing to watch out for is to not drill into your tank if mounting to the floor of your trunk
Also, many people like to make or buy amp racks, and place their system in a way so that it looks like it could be shown at competitions. The trunk allows for much more room to make amp racks and custom enclosures.
A disadvantage is trunk temperatures. Although for the most part, amps are made to operate at hot temperatures (hot is open to interpretation) sometimes lower line amps or non-fan cooled amps will overheat during the summer. Trunks generally don't have much ventialtion, so air is not circulated away from the amps area as fast as it is heated up. This can cause the amp to go thermal after a little while of loud playing.
Another disadvantage is the cost of the extra wiring. pretty cut and simple.
Also, signal is open for more interference as it is run for longer lengths. Depending on where you run your wires, it can also pick up interference from other wires you have run close to them, but this is becoming a rarity as wires progress.
So basically, as I see it in my opinion, if the amp fits under your seat fine, it is a better location to work from unless it is too cramped and not properly ventilated. The underseat instal may take a bit more time to get in correctly. It also opens the amp for damage due to persons/items carried or flying around your car.
Trunk installs are generally the norm, adn there are more people who have done them and can provide help during your own install. The amps have more room to be installed, although there is a slight risk of interference and more chances to run into pinched lines if not careful.
I have my amps installed in the rear BTW //content.invisioncic.com/y282845/emoticons/wink.gif.608e3ea05f1a9f98611af0861652f8fb.gif