Paolo,
You might check the .sopc_builder file that is placed in the user's home directory. I *think* this is where all the SOPC Builder settings are saved to. If your kit installer can modify this file it should be all that is necessary.
By the way, your kit idea sounds interesting. Do you have a website where this is discussed? What sort of add-on components are you thinking of? If it is not something that can be publicly discussed right now I understand -- but when the time is right I'd like to see what you're doing.