I agonized over what to do for subs...I looked long and hard at the factory style in the rear back of the hatchback, almost bought a used one on fleabay, but didn't think I'd be happy with the bass performance. Would have been nice to do a custom style moulded enclosure that looks like it belongs as part of the car, but life gets in the way, so I ended up buying a sub amp for under the seat, and just a vented box sub for the back, on banana jacks so its easy to unplug and remove if I need the space

 

If money isn't an issue, JL Audio makes a Stealthbox for certain model Velosters. It probably won't have as much bass output as 2-12's but should be noticeably better than the stock sub.

I myself just did what you said, threw a big box with 2-12's and an amp in the hatch. Yes I have lost most of my cargo space but if I need to do anything that requires space in my car, I put it in the backseat or I just take my wife's Sonata. She only has 1 10" sub in a small box in her trunk so there's still plenty of room.

 

I went the JL Audio way... 13” Stealth Box and it sounds great with the Dimensio Audio ?

just to show example...