How to give different colors to duplicate composition in after effects?
What you need to do is:


clone the layer, 
right click and choose View Layer Source in Project, 
duplicate the source in the project window, and finally 
alt/option-drag the new source on to the (selected) cloned layer to change its source.


If this is too tedious, I've written a script that will clone the layer and create a  unique source for it in one step (it can also recursively clone all the source layers in compositions if need be). There's also a pay-what-you-want script called true-comp-duplicator on aescripts.com that will do the same job.