Soak all you can with towels and such. Then sprinkle some baking powder on the damp area to help prevent smells and molds. It'll be white for a short while, but once it is all dried out you'll be able to vacuum it all out.
Park in direct sunlight with doors/windows open and even run the floor heater setting to aid in evaporation.
I will be changing out my stock sub for a amp+sub. If you want me to keep you in mind I'll pass on my stock sub super cheap.
I wouldn't worry so much for the engine as opposed to all the internal electronics/wiring. Check all of your fuses, especially the constant power fuse.
If you don't mind me asking. Did the water just work its way in or were the windows possibly cracked or did it rise to the base of the door and seep in? Best of luck.