Should capex and expenses be kept in separate accounts  form your personal cashflow?

I have a Mother/Daughter home in Middlesex, NJ that has a separate, private entrance for the second floor apartment.

I consider this two separate topics: 1) what does the property need to make it rent ready?

They are completely separate buildings (500 ft. apart) but share water connections, entrance easements and such.

I think it is best to separate the two issues. 

Further the idea of "saving" (cap ex) money for a roof, seems silly unless you are actually going to put the money in a separate account.  

In regards to renting by the room (house hacking a sfh), this strategy would typically bring more rent than just renting out the entire house to an individual.For example, median rent for a 4bd/2ba house might be $1850 but if you rent it by the room (individual lease for each tenant, each tenant pays you separately) you might be able to get $500/room or $2000 for the entire house.  

Rather than just correcting the permit, we decided to split the building into three separate condos.

That way each property has its own separate books and records, its own insurance, its own bank accounts, resulting in no legal exposure to the other properties, nor co-mingling of funds between properties. 

Old 1961 house, with separate entrances to the upper and lower level; I suspect it functioned as an actual duplex at some point.