When you replace the battery get a larger capacity one with more cranking power. You might find one battery keeps going flat depending on how powerful ur system is. The wheel cavity is a good idea. Jack the car up on that side to give you more space to move around. Don't drill through the brakes or suspension though
Fill the hole with mastic.
Otherwise as Waynne suggested drill through the bottom of the car in the footwell but again mastic the hole up to avoid rust and water damage.