Not all decks have options for subs. But all decks will control the volume of the subs if hooked up correctly.
And as for running the wires, there is a large rubber grommet around where the steering column goes through the firewall. Get a utility knife and stab it through the grommet, this should give you a place that is easy to access from both sides of the firewall and easy to actually put the wires through. It is also the safest option if done correctly.
But I seriously recommend getting a friend or someone who has done stereo installs before to help you with all of the fine tuning to the amps and deck and the break-in time etc.