How to overcome an informal organization administration and get evaluated and compensated justly ?

I cannot understand what you mean of "informal organization". Or is there a formal organization? Perhaps you are trying to say about organization that has no clear system on how to evaluate its employee as to how they are effective in their job to use this evaluation for increment. I hope i am in the right frame of mind otherwise you can ignore this answer.

See, if you have this kind of system in the organization, you can do2 things. First, question the management on how they come up with salary increment. What are their basis? But of course I don't need to tell you how to do it to maintain good relationship with the management at least to ask them in a very nice way. Next, if, despite the effort you were not able to get yourself satisfied with their answers from your questions, the best thing to do is to be the best of what you are at work and with your colleagues and not to expect much. If you reach the point where you are no longer satisfied with what you are doing then resign gracefully. This way, you retain peace in yourself and you leave peace from that organization. So finally, you had overcome the situation. 

JUSTICE is last century word,, in real world personal liking & disliking matters a lot so dont expect novel like bookish sentiments in2014.