I cannot get my cakes from my sims inventory to set on the bakery shelf. Arent they supposed to sit on the very top? And when I go into buymode from the commercial lot, there are no cakes there for me to buy. So, I had my sim bake them herself, but, they still wont go onto the shelf.
And final problem I've noticed is that I have no way to program what the register sells. In the youtube video Ani has for her savvier seller, shes able to open the register like a bookshelf or refrigerator and put things in it. I cant do that... Am I missing something?
Is it ok to have the Industrial Oven and the Bakery Shelves and register on the same lot?

Bakery displays and racks have to be loaded while in Build/Buy Mode, they can't be loaded from Live Mode. Of course, you can't reach a sim's personal inventory that way, so you have to put the items down on a usable surface first as I recall. Or the floor, even. Don't see why an Industrial Oven and a Bakery Display can't be on the same lot.

Can't answer the Savvier Seller problem, but am sure there are others here who can.

Ahh ha! I didnt know I couldnt load those racks from live mode, I was able to drag vegetables into it without being in buy mode, and 3 pies. Then, when I got to the cakes, it quashed my groove.
So, when I am in buy mode, do I just drag things to it the way I would in live mode? I assume clicking the bakery shelf to load it would just cause the hand to pick it up as if I wanted to sell it, so I will try just dragging.

What about the registers? ani's mod shows being able to click it open like a bookshelf, but I cant do that.

You click on the item and drag it to the slot you want it to be in on the Bakery Display or Rack. If you are lucky, it will land in the slot you had intended. The Displays have to be loaded or unloaded from behind, though that may not be necessary for the top shelf since it's exposed. Again, someone else will have to answer the register question as I don't even have the store set let alone the mod.

Still could not place a cake on the top shelf in buy mode, even if i flipped the display around. Strange, that's ok, I dont need to sell big cakes then. I will focus on the bread and pies, which I found I do not have to go into buy mode to place, they just drag right to it. Setting it in the precise place doesnt work as well as it should but, thats the least of my worries at this point.

@ladybarefeet: In that video, Ani is showing her cloned versions of the EA Bakery Set objects (Shelves, Display and Register) to which she has applied her Savvier Seller script using S3PE. She cannot release these publicly because they are Store Objects.

There are instructions on how to do this at the bottom of The Savvier Seller FAQ page but they are not for a beginner and if you have never used S3OC or S3PE, may be a little hard to understand. If you want to try though, let me know and I'll see if I can find alternative tutorials.

Just had another thought. You can always use the existing savvier seller objects (Register, Shelves and Display Pedestal) to set up a bakery. Or alternatively, Sandy from Around the Sims 3, has many displays available for this purpose here. Just make sure you download the savvier seller versions using the second, smaller download link under each object.

I wonder if maybe I wasnt using the register from the mod. I do have a package file from here that has shelves and rugs and things in it. Maybe I just wasnt careful and added the wrong register, but I only recall seeing one, which would follow your idea that she might not have released hers.

Ahh, she did include her register for savvy seller, but not one for bakery. Darn!