Certainly you will have doubts. There will be questionings and faith will return again. That is how faith is established.
Pray to God with tears in your eyes whenever you want illumination or find yourself faced with any doubt or difficulty. The Lord will remove all your impurities, assuage your mental anguish, and give you enlightenment.
No doubt, God alone has become all these objects, animate and inanimate, but in the relative world all beings act and suffer according to their past Karma and innate tendencies.