I agree, the 2nd floor may not be the best place for a HT, especially if you have kids. Placing a door may add some relief as the two bathrooms/walk-in add some protection i would imagine.
Can you finish your basement? If you are low on dough, but still serious, then one option may be to make just one room in the basement for HT then expand when more capital becomes available. Just a thought.....
As far as arrangement, could you not place your TV on the bottom wall (towards master bed.). If it is 13 ft, that would be sufficient if your TV is even 40-45". Then the rear speaker placement would be easier. Again, just a thought.