I asked this question in the clan forum and it was suggested that I bring up the issue here, so I have. Below is the orginal question and first responce:

I have joined a couple of clans, what owuld happen if one clan challenged the other? Would I have to play against my own clan or would I be exempt. The reason I ask is if you had more allegence to one clan than the other, you could possible lose to help out one or the other. I would never do such a thing!!!, was just wondering.

Reply by tejo
It simply can't. You cancot challenge a clan who has one or more members that are also in your clan. BTW I hope this will change soon, by just excluding the members who are in both clans

Thanks