Jesus’ instruction to Thomas was "Stop doubting and believe." Jesus calls us to develop a permanent attitude of openness and trust toward Him – not just to be open to him and trust him on any one occasion, but to be like this ALL the time. Yes, at times the Christian life is a lot like walking in the dark. The dawn is now nearer than when we first began to walk, but it is yet to happen. We cannot fully see the road ahead of us; we can’t see the full picture; nevertheless we trust in the Lord to guide us. "For we walk by faith, not by sight (2 Cor.5:7)." This requires us to accept uncertainty.
"Faith is taking the first step, even when you don't see the whole staircase." [Martin Luther King Jnr]
Some steps to take: Read the Scriptures, as faith comes from hearing the Word of God. Read or listen to the stories of other's people's journey of faith. The writings of C.S. Lewis are especially helpful as he was a person who came from atheism to faith and in doing so had do deal with the questions so many of us ask. Read the spiritual classics. Do some good study in apologetics – which can help you answer your own questions. Check out the writings of Ravi Zacharias, Alistair McGrath and N.T. Wright. Discipleship of the mind is essential.
Keeping a spiritual diary can help too, as you follow and reflect on your own journey of faith in Jesus.
[These thoughts on doubt have been gleaned from Alistair McGrath's excellent book Doubting]