Science certainly can deal with the existence of a God, many Gods or whatever. If there is observable, testable, reproducible evidence for the existence of anything we can look at the data, test how it fits with what we already know and then formulate a hypothesis that includes the existence of God. If this data is then tested again, reproduced via experiment and observation and the hypothesis stand up then it will become a theory and await disproval, which might or might not happen depending on what we learn in the coming decades and centuries. It will of course need to published via the peer-review process so everyone can judge for themselves.

At present, I believe there is no empirical evidence that points to the existence of God, or a whole pantheon of Gods. Not a thing. The empirical evidence for evolution is however, substantial and the theory has yet to be challenged in any meaningful way (that's not to say bits of it aren't challenged as more data comes to light; the theory as a whole is quite robust).