You can still believe that the scientific method works; and might leads you to 2 conclusions:
(a) "I can prove earth is not flat" (using this methodology) (b) I cannot prove there is no God, though I may believe the prevalence of evidence does not support the hypothesis, there's no scientific test that I can design.
The scientific method is partly inspired by belief in a God who is good (so no deceit) and created a universe that runs on laws. If you have particular beliefs about God, you can build a lot on that (as Descartes did).