Re: Transposing
Steps1 & 2 are correct Of two 2 tones how can I chose the correct one I created 2 new staffs and wrote the birthday song " happy birthday to you" both in the key of A and the separation still exist 
If you have 2 IDENTICAL staves, BOTH in "A" and the playback of each staff is different to the other then I can only suggest the "Playback Transposition" of at least one of them is wrong. Check the "Instrument" tab of the properties of both staves. Until you actually do a transposition, the playback transposition of both should be 0.
Once a transposition is done, the playback transposition of the transposed staff should be the OPPOSITE of the transposition performed.
E.G. if you transposed UP 9 semitones [+9] (for an Alto sax, say) then the playback transposition should be -9, that being the difference between the transposed key and the original concert key.