If you're trying for a somewhat even gameload between the two clans (say 12 games for each), there's currently no way to manage that other than informal agreements with the clan leaders involved. And even then, they each need to remember those agreements without any real support in the software when making/accepting challenges.
Example: If you have 6 games for clan B but already have 15 for clan A, it's quite possible putting/leaving your flag up will result in even more games for clan A. Leaving clan A would certainly fix the problem, but the clan challenge flag proposal I'm making seems like a more appropriate response.
There are a lot of ways to approach this, including leaving and later rejoining the clan. Allowing players to set a max games setting per clan similar to their site max game would work as well. The dual flag approach just seemed more doable to me and more to the point, so that's what I'm suggesting.