To all: this is continuation of discussion started on another forum server, I asked angelguy to move here

As you might be knowing the pH computed by BATE was 4.69 without the activity coefficient and 4.44 with activity coefficient..
Well, when I trying to understand the actual calculation behind it. I figured out in equilibrium composition section that the pH computed was 4.31. Could you explain what is the difference between these pHs. i.e 4.69 and 4.31.
4.31 is -logarithm of just concentration. Remember, that pH is defined as activity scale. 4.31 is a result that you will get measuring H
+ concentration with spectroscopic methods (if they exist, can't remember any suitable).
When the H conc(computed by 4.31) multiplied by the activity coefficient of h3O+ ions gives pH of 4.44. Could you please explain me by which equations other Ph like (4.31) comes.. 
4.31 is calculated exactly opposite way - first, acitivity is calculated (numerically). Then, activity is divided by the activity coefficients to give real concentration.
and why did we used phosporic and pottasium hydroxide instead of the actual ions.(H2PO4- and H3o+)??
To overcome limitations of the user interface - at present it doesn't allow to enter salt concentration, but it allows to create any mixture of acid and base. Potassium dihydrogen phosphate is nothing else then equimolar mixture of phosphoric acid and potassium hydroxide (once the neutralization reaction ends, but it is very fast).
Actually, I tried computing the complete thingy by activity coefficient. Let me give the detail of it,,
I computed the Ka'(Ka with activity coefficient ) by multipying Ka (original, 7.2) with the activity coefficents of H2Po4(-), HPO(2-), H3O+.
Don't ever do it. Ka is defined and measured using activities, so there is no need to modify its value. Instead, do the calculations using activities.
It is not easy to calculate activity coefficients for acid/base equilibrium by hand. Why? Because that's iterative process. You start with classical calculation of concentrations, then you calculate ionic strength and acitivity coefficients, you put them into Ka equation, you calculate new concentrations and you repeat the process untill the results of two consecutive steps differ less then predefined treshold.
In your case (KH
2PO
4) situation is rather simple, as you may start calculations assuming known concentrations of K
+ and H
2PO
4- and calculating ionic strength and activity coefficients using these values. H
2PO
4- dissociation is so weak that it will not change ionic strength of the solution much (abundance of K
+ and H
2PO
4- creates so called ionic strength buffer). Thus one step of calculations should be sufficient.