I'm not 100% sure, but I'd say start with only 1 business download, and it should ask you later if you have a 2nd business, whereby it may ask you to purchase on-line... This way it links it properly. Speaking more from experience with a (one) Home & Business CD upload (which comes with Fed.+ 1 State filing) that later needed me to add a 2nd State filing for my particular case, and allowed me to purchase on-line while I was running the initial (one) program.
