I imagine you have already solved your problem since one year has passed!! Sorry to see that so late!
But sequential FISH is quite simple and robust. You just have to hybridize your first probe, then you remove your first probes under denaturing conditions (70% formamide-2SSC), dehydrate your sample, and rehybridize it with the new probes. I can give you a more detailed protocol, if you're still interested.