Hi Rex and welcome to our Forum!
You can't mix residences and business like you mentioned. The stores are rabbit holes at the moment, meaning we don't even get to see the inside of them when a Sim shops. Same with the business where Sims have jobs. However, I've read that the upcoming expansion pack, World Adventures, will have sales counters where you can purchase items. I don't know that you'll be able to have a residence on the premises, though. Another thing is that you can be self-employed in the Sims 3 by being an Artist or Musician. You can also earn money from Gardening and Fishing. It's not the same as what you're asking, but it's possible to earn a living inside the home and on your own.
I hope this is helpful to you!