[Possible Stupid Question] Renting the house vs renting rooms

[Mitchell Sanedrin]

Hello!

Per Brandon Turner's advice in his "The Book on Rental Property Investing" I've been allocating a few hours a day to analyze some properties using the BP's "Rental Property Calculator". 

I've found a few homes (Located in the SF Bay Area) that caught my attention and have tried analyzing a few of them (all resulting in negative cash flow). I've used Zillow, Rentometer, and BP's "Rental Estimator" and there were times that I'd gotten a wide spectrum (at least to me) of suggestions for what the property WOULD rent for.

Ex. Property A (3BD/2BA) would rent for 2000 (Per Average of Zillow, BP, Rentometer).

I've tried exploring craigslist also, and have found individual rooms (in a similar condition/style of home etc.) that are close to the one I'm interested in with roughly $800/room resulting in a total income of $2400.

Running the calculations with "Property A" with avg. rent of $2000 resulted in negative cashflow. Running the calculations with "Property A" with avg. rent of $800 was positive. 

Two questions then I pose from my experience:

 A: Am I doing something completely wrong with the calculator that keeps giving me negative cash flow, or am I just not finding good enough deals?

B: Which "estimate" in regards to rent should I base my math on? (rental estimators for renting the entire home v. renting the rooms individually). Living in the Bay Area, CA I've seen some pretty outrageous prices for rent which is how I came to this "challenge". 

Apologies in advance if this may seem like a stupid question to bring up--just lost and looking for a bit more guidance. 

Thanks in Advance!