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.

Yes.  Turbo Tax Business can prepare many business returns and different kinds, 1120, 1065 and 1041 returns.

For federal you can use one Business program.  You have to buy the state Business program separately from inside the federal program.

Preparing state tax returns for more than one business?
When they are the same types of businesses (such as two S Corps) and file taxes in the same state, buy one product and use for all at no extra charge. Business State efile included.

When they are the same types of businesses (such as more than one LLC), but file taxes in different states, buy one product per state for $49.99. Business State efile included.

When they are different types of businesses (such as an S Corp and a partnership) and file taxes in the same state, purchase one product for each business type for $49.99 per each business type. Business State efile included.