I'm no expert, but here goes (sorry if I misunderstood the question and this is too simplistic!!):When an Alto Sax player plays a "C", it sounds as Eb in concert pitch...which is why it's called an Eb instrument.
When it comes to notation, the Alto sax part is usually written one major 6th above the actual (sounding) note. So, to hear a Middle C, you would notate it for the alto sax as A above Middle C etc.
You can also apply this strategy to the key signature you use; ie if the sounding key is C major then you notate in A major.
By the way, tenor saxes (Bb) are notated a major 9th above the concert pitch; soprano saxes (also a Bb instrument) are notated a major second above the concert pitch.
(The easy way to do this in Sibelius is simply to add an Alto Sax instrument to your score, notate it in concert pitch, then when you've finsihed, click "Transposing Score" on the Notes menu. Let Sibelius do the work for you!!)
Hope this helps!
