The only problem with doing 2 different bass systems is you are going to have serious frequency overlap which is going to cause response hot spots. Plus, since you will have two different sources that are so different you could run into phase issues. The only way to solve that is to take and EQ or Crossover the hell out of the system’s low end. The problem is playing one type of music or movie it's going to be ok, but with something with a different bass structure it's possibly going to be flaky and not natural at all. Plus, it’s going to take forever to get it dialed in just right, and it’ll never be 100% matching.
The large tower or just large bass box idea is a good one, and so is the IB setup but they both have their different properties. I would only go with one and not the other. Personally I would go for a large ported box with a 15” and an 18”. I also wouldn’t go with a car audio sub; I would go with a Pro Audio sub, just for quality reasons.
Nothing against the car audio sub, I am just throwing some ideas out here. I think you need to ask yourself am I going to use 15Hz enough to throw money into a system designed for a 30Hz spectrum. If you are GREAT for you, but I don’t see the need, anyway, it’s all about having fun and if you are and it sounds decent then perfect.