mythbuster =>
Using a db prefix to differentiate the two stores WILL NOT accomplish what you want, flyerguy. Here's how that works.
If you have a hosting account that allows only one MySQL database, you can run more than one spearate stores with the one MySQL database by using a different prefix for one of the stores. This will create a whole separate CubeCart installation, so there will be two sets of CC tables in the one db. One set without a prefix, the other with a prefix. This is the same, in effect, as having two stores on totally separate databases. If your hosting account allows you to have more than one db, you may as well just have separate dbs on these two stores. It is the same effect.
NOW. As to having two stores on one database, sharing the same exact tables . . .

Of course this can be done. I do it quite regularly, in fact, when upgrading stores for folk I will often have a brief period when
mystore.com and
mystore.com/newStore will share the live db ~ but in those cases, I don't leave them both on there for very long. This is the scenario that flyerguy refers to. As to having a completely different look to these stores, that can be accomplished very easily by having a skin at store A and a totally different skin at store B both with the exact same name

From there it gets much more difficult, though. Running two separate stores from the one db will run into other problems, and will require some modding to make it work. Everything you set on the store's General Settings page goes into an array saved to db - so the stores will have the same store names, along with all other settings. They will have the same admin accounts, etc. etc. etc. So basically, there is no easy answer or solution for this. If you have to ask, you probably can't do it for yourself.
There may be other solutions you could explore for what you want to accomplish, other than using two stores from same data.