This is new functionality that I have not used. You'll have to test it and see how it works. My understanding is that if you maintain the same TIN for multiple company codes and mark the box discussed earlier, then the system will combine the 1099 items for both company codes together.
But you might want to ask yourself this; Do you really want to combine information from companies with separate TIN's? I'm not an IRS/Tax guru but this doesn't seem like a good idea. I'm also fairly sure that when you submit files to the IRS you have to submit separate files per TIN.