You should be able to point to your Zen Cart from other parts of your site, but using it as a back end only will take lots of work and probably isn't worth the effort. You're better off letting Zen Cart do the work. Reinventing the wheel isn't necessary.
Unfortunately, lots of people get bogged down with details they don't really need to mess with and miss how simple Zen Cart is to set up and use. The learning curve is steep, but not impossibly so and once you get past it, you won't understand why you thought it was so difficult.