you can also do that but it's more of a "just in case" thing than a necessity. i generally have them separated as well but that's also because i don't want to have too much stuff crammed in there in case i go 1/0 gauge later on.

the ground wire will come in the kit. basically you can either drill a new hole and sand off the paint for it or you can use the bolts that hold the seats to the body. you also have to sand the paint off the seat bolts but it keeps you from having to drill.

rca wires are these http://www.sonicelectronix.com/item_68336_T-Spec-V6RCA-172.html

they are the wires that carry the audio information to the amplifier. the 4 channel amp will use the front+rear rca sets and the subwoofer amp will use the 3rd set.

remote wire is a remote turn on wire. basically when your head unit gets power it tells the amps to turn on through this wire.

power wire installation generally goes like this:
attach power wire to battery with the in line fuse near the battery.
run the power wire for the subwoofer amplifier on whichever side you are installing the subwoofer in the back.
run the power wire for the 4 channel amplifier towards where you are installing the amplifier. if its going to go under the front passenger seat then run the wire to the passenger side for example.

when you run the power wires you will either need to drill a hole for them to go through the firewall or you may have a place to run them with other wires through the firewall and you won't have to drill anything.

the rca and remote wires go from your head unit to the amplifiers. so run the rca+remote wire for the subwoofer with the subwoofer wire and the same goes for the 4 channel amp wires.

to hide the wire you remove the plastic interior pieces around the edges of the carpet and put the wires in there and cover them back up. this is optional on the 4 channel since it will be wires pretty close to the front of the car usually and hiding an 8 gauge power wire under the floot mat is easier and accomplishes the same end goal.

the new speaker wire will basically go the same route as the old speaker wire into the door but instead of attaching to the head unit it will run to the 4 channel amplifier.

and ask any questions you feel like. i'd rather you not have any problems with the install and maybe one day you can answer all these questions for someone else wanting to install stuff and help them.

also on the power wires when you are hooking them up make sure the fuse isn't in them. you don't want any power in the lines until you're done with the install.

if you do get around to running the others amps wiring don't forget to yank the fuse.

the in line fuse on the power wire. this will keep it from shorting out if it touches metal while its just sitting there loose.