Where should I start laying nail down hardwood flooring and how do I make it straight?
First, remember to lay your wood perpendicular to the floor joists. Laying it parallel can cause a waving effect which is unpleasant.

Next, find the longest, longest, straightest wall which is perpendicular to the joists.
Measure out two feet from the wall all the way down the wall.
Then find the best line down these marks, snap a chalk line, 
Measure back to the wall about 23 and 5/8 inches. Snap a this line. 
Line up your first run of floor against this line, tongue side out (nail through the tongue).

As for room to room, if they are really out of square with each other, try building a transition between rooms:

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This allows you to lay each room separately, allowing each room to be square.