In this quote Eli is talking about what Moishe The Beadle told him. It is an example of foreshadowing. Later on in the book he is asking God why he is doing all of this and God does not reply in a way that Eli will understand.
Man comes closer to God through the questions he asks Him, he liked to say. Therein lies true dialogue. Man asks and God replies. But we don't always understand His replies.
For the first time I felt anger rising within me. Why should I sanctify His name? The Almighty, the eternal and terrible Master of the Universe, chose to be silent. What was there to thank Him for?
Eli is marching on the railroad towards the pit and is questioning God for why he is doing this to him. This is one of Eli's first doubts about God.
Eli and his dad were crammed in a tiny building. He thanked God for making mud because it was hiding his new shoes from Kapo who was taking everyone's shoes. This was a sign of faith being restored.
I thanked God, in an improvised prayer, for having created mud in His infinite and wondrous universe.
It is the eve on Rosh Hashanah and before they eat they said a prayer. Eli is overwhelmed and feels betrayed by God. He does not understand why God is letting this happen.
Why, but why would I bless him? Every fiber in me rebelled. Because He caused thousands of children to burn in His mass graves?
It's over. God is no longer with us.
Akiba Drummer left the camp and had died. Eli talks about how Akiba had lost faith in God and then talked about a time when the rabbi had lost faith in God. This showed that Eli was not the only one religiously effected by the effects of the Holocaust.
And in spite of myself, a prayer formed inside me, a prayer to this God in whom I no longer believed.
In this scene, Rabbi Eliahu asked Eli if he had seen his son. Eli responded no and then had realized that he did she Rabbi's son, but his son was running, not waiting for his father. Eli was glad that Rabbi had continued to look for his son. Then, Eli prays, asking God to give him the strength to never do what Rabbi's son did to him. This shows that even though Eli does not believe in God anymore, he is giving God another chance to answer his prayers and shows that he still has a little bit of faith even though he says he doesn't.