How do you separate tasks?

I can tell you that it is best to always have the option to buy the house separate from the lease. 

Do I setup separate accounts for each property?

Should we view each unit separately or just view the duplex as one property since it’s under the same roof?

We each did one separately this last fall and those worked out well.

Upper floor has 3 bedrooms and a bath and lower has a separate entrance with suitable space to make into a 1 bed apartment.

I believe most of these other items remain grandfathered, though I'm assuming you mean by "fire doors", doors that are supposed to be used for fire separation, and not a separate means of egress (because those are usually required).

What yields the most income tax return, file married separately or file jointly?

My question is, are we better off filing married jointly or filing married separately?

Speaking of LLC, it seems that the biggest issue with forming an LLC is the up-front work to do so and the separation of the financials?