What do you mean by upgrading the database? I already have the latest, so there is no need. I don't have an old version like you said, this was a brand new install of Zen Cart and the database. I guess when I created the site it duplicated the tables, one with the prefix and one without.

Yes, my database has products, pricing, etc etc... in it. That's why I need suggestions on the best way to handle this.
I guess I'll need to manually (and tediously) copy and paste from the wrong tables to the correct ones, then delete them after. Ughhh...

So the instruction to place data in the prefixed tables come from the configure.php files? Ok, I will fix it there too so from now on the data is going where it is suppose to.