Hey there, I want to hook up a subwoofer in the back of my van under the bed, which means running power and signal wires. What is the best route to run this stuff? I know I need to keep the signal and power wires separate.

As a side note, I will be running a 0/1 gauge wire and hope in the future to hang 2x house batteries under the vehicle so I want to make it somewhat easy to do. Thanks

Run the power lead outside, under the van, strapped tight to the frame and clear of heat, always use a grommet when passing through metal, keeps it from getting cut.
I have a battery in the rear of my van, linked to the front for charging the way I explained, the amps for my stereo are under the rear bench in the back, tied into the rear battery, RCA feed goes down the drivers side, against the wall to the amps. Brand name, heavy insulated RCA cables are the only way to go, not cheap, but low signal degradation, and no interference, 18 gauge speaker wire is fine, unless it's longer than 20 feet, you aren't gonna notice a difference with heavier wire.
Be aware to get the best sound, your sub requires a certain amount of airspace and firing in a certain direction for optimum sound quality.

Thanks for clarifying. In terms of getting the signal wire from the front stereo to the back, what is the best way to get it back to the conversion part. Through the roof, door frame, or floor? Cause unlike my old car there is no real door trim to run the cable through.

Hard to answer that one. It looks like you have a conversion van, there should be plenty of wood, carpet and paneling to tuck it under, but every brand is different. You could try posting pics of your interior but it still might be hard to see. I would just try to plan it out. By carefully take bits apart and seeing how it's put together you will learn a lot about your van.

Mine runs between the doghouse and console then down to the floor between the seats. Tucked under the carpet. Under the drivers seat. Over the the driver side wall and tucked under it where the wall meets the floor. See if that helps on your van.