Mainly fire barriers, and extra insulation in between the floors. you could go with permits for the work that is being done if you want to avoid any concerns, but as far as the city will be concerned your home is just a single family that has a Mother-in-Law suite, and you are renting the spaces separately.

I will continue in my current W2 job for at least two more years, and that job ties to a separate 401k. 

When using the landlord app I'm unsure how to use for (eventually) multiple properties that will also be in their own separate LLC. 

Usually the best situations are the ones that have management companies with in house separate departments for each of these scenarios.  1 person doing it all can lead to a management issue in some cases.

Here are the details: Purchase Price: 400,000-425,000Single family home with a mother in Law suite in back; as configured now its a 3bed/1bath and a 1bed/bath; Will configure turn the garage into studio w/ bathroom, so essentially will a total of 5 bedrooms and 3 baths (as 3 separate units) after renovation.

You may have to get separate quotes from contractors also.

As far as questions you can get a pretty good picture from:1) are utilities all separated?  

Here you go Great answer I don’t know CA law is the landlord required to keep your deposit separate and notify you where it is kept?

I am a first time home buyer and am planning to put an offer for a duplex which has two units separated by a wall.

I have never seen the inside of this wall that separates the laundry room from kitchen.