It really doesn't matter how you mount your subs. Polarity of the subs does significantly matter, however.

If you invert your subs, you will want to wire these guys in reverse polarity. This way, when the bass notes hit, the sub will fire "back into itself" and will give you correct phasing.

It you invert one sub and keep the other mounted in the box, you will want to wire the sub in the box "in-phase". The inverted sub will be wired "out-of-phase", which will put the car acousticly "in-phase".

Unfortunately, most people do not understand phasing in a vehicle.

In our particular vehicles, most of us install component sets into the door and dash. This does great, but phasing often comes into play. It's been my experience to wire the passenger woofer "out-of-phase".

Why do this, one may ask. Well...firing each woofer in "mechanical" phase doesn't always mean that the audio system in "acousticly" in-phase. You need to listen to various frequencies to determine the best phasing for the car.

Proper acoustic phasing is more important than proper mechanical phasing.

Good luck to you!