You do an analysis to estimate the value of the second unit, and subtract that from the duplex sale price.

(NOTE there are some additional additions and subtractions that go into calculating self employed income. 

Then subtract that from your offer just for starts....1) Approx $20k ($10-40k)2) $4k, you'll want a liner as well3) $8k4) ^^5) $25006) $6kThese are rough since I haven't seen the house, but you get the idea.....

But do they go off of overall net profit after subtracting repairs/upgrades that are claimed to each property.

Not sure how that calculates as a normal rental where you could just subtract rent from expenses and set aside some for maintenance, because the act of renting it out allows me the zero rent at the apartment.

Cash flow is calculated by subtracting out all your expenses from your gross rent and that's cash flow.

Profit is a specific calculation which is the adjusted cost basis (acquisition price+capital improvements-depreciation) subtracted from the net sales price (contract price minus closing costs not including loan payoff).  

It is calculated by subtracting you purchase price and cost of improvements (basis) from the end sales price.

Once you have calculated those costs you subtract them from the stabilized value and that should give you the current value. 

All you need to do is track the readings, subtracting most recent from the last to get your usage for that unit, which you subtract from the usage on the main meter.