I don't want to discourage you, just point out what little proffit I've recieved, I've recieved by mining one pool steady.  The only way I've gotten anything to mine a 2nd pool is to have more hardware on a different pc do the mining OR a new terminal window and one for the GPUs, one for the ASICs.  With how the S1 is, I really doubt you can start a 2nd instance of it from the console to have half of it mine one pool and the other half mine a second pool.

The only option I can see from here is get a 2nd S1 and set it to the other pool.