Then that total is subtracted from your total expenses for the year.

I've yet to see someone say: "I have "x" but I'm subtracting "y" to keep as a reserve fund and planning on 25% down".  

Take the value that the agent gives you, subtract 30%, subtract repairs amount (guesstimate), subtract your profit.  

We have a commercial general liability policy that is pretty easy to add and subtract properties from, and I'm looking for something similar for damage coverage.

Subtract 6% for transaction costs and $125,000 for the remaining mortgage debt, that leaves you with $260,000 in equity on your $60,000 down payment + call it another 10k in closing costs. 

Take your $1000 cash flow, then subtract $100 for management that you stated and 20% for future vacancy, maintenance, and capital expenses.

Don't guess.2 - Subtract all the cash you get back over your first year.  

If you talk to her and say, "You know, I think it's probably worth $175K after it's all fixed up, I think it will take me $60K with with all the known and unknown work, plus 6 months of my own time (@$4k/mo), interest on the loan, insurance, permits, etc etc, so subtracting that from the final value, I can offer about $50-60K." 

It was a matter of subtraction and rerouting.

Beyond making more money on the SF houses over unfurnished rents, it depends how much more you make for your time (after subtracting all your hard costs of course).