We have plans to create first multi-algo switching ports on NiceHash, so your miner would automatically mine Scrypt, nFactor or X11, depending which one is more profitable. The only issue for now is that there is no united miner supporting all algorithms with ability to define algorithm per pool. Once this is solved, NiceHash will support this feature and you won't have to look at tables and adjusting your miners anymore.
When you get me a JSON API I'll see if I can give you a Windows app that will control the miners and restart them with the proper algorithm. I'll bet I can talk the PiMP team into supporting the same for Linux!