clickwir- I really wouldnt worry about noise when running a SUB RCA next to a power lead... the noise that is usually heard is a higher frequency "whine". The shielding really wont make much of a difference, and none at all with subs.
My guess is that if you had your equipment in a 3rd gen accord, it'll fit in your prelude just fine.

smakdown- the most crucial parts of running a power wire are the fuse, and to make sure that nothing will chaff the wire, especially at the firewall... make sure to use a grommet there, instead of just drilling a hole. In my 94 accord, I found a place, just under the heater core where I was able to drill a hole and fit a grommet in... in the engine compartment, it came out just under an air canister attached to the firewall, which the canister just slid out of its bracket, so it was very easy to get it out of the way to make the job easier. Again, make sure to allow for a large enough hole so a grommet will fit, try to find a grommet that is relatively snug on the wire, so there will also not be any air or water leaking in. In the passenger compartment, its really easy... those sill plates just pop off, as well as the other trim pieces... running the wire in some split loom tubing is a good idea, and an extra level of protection against chaffing. (this is the black plastic sleeve found on most of the cars factory wirring, and can be purchased at lowes) Likewise, use it in the engine compartment... not only will it look a lot better, and more factory... you'll protect the wire from the elements, as some wire is not nessecarily gas and oil resistant... these can deteriorate the insulation on some wire over time.

For the ground, you will ground the amp in the trunk, as it is best to keep ground wires as short as possible... as well as using the same or larger gauge wire as the power wire. Try to find thick metal to ground to... and keep it close to the "frame" of the car, I like to ground directly to the frame. You'll find 2 frame rails in the trunk, to the sides of the spare tire well... prep the surface well by removing the paint... I use stainless steel screws or bolts, that can be found at hardware stores, so they do not rust... then coat the exposed steel and connection with some clear coat, to further prevent rust.

Haha, I take a lot of, some say "extreme", measures... but it makes a world of difference in how long the set-up holds up.

Run the wires right to the rear speakers, for the easiest instalation... doing this also eliminates the need for a remote turn on wire. The pre-amp output your deck has, can be used, if you like... but tapping into the rear speaker wires will probably be more convient for you, I would say you'll get the same sound output.