If the apostle Paul prayed for his country, if salvation is a work of the Spirit, if Satan is at work to blind the minds of men lest the light of the gospel shines on their hearts, and if we are to pray for an effective witness, then certainly, due to our own inability, we must pray. God is sovereign, but in His sovereignty, has chosen to use us and our prayers to open doors and hearts and to bring people to the Savior. Can we understand this? No. The fact is the Bible teaches both the elective work of a sovereign God and the volitional responsibility of men. This has often been called an antinomy, a contradiction between principles or conclusions that are equally necessary and reasonable, but defy our ability as finite man to reconcile them.
An excellent book on this is Unraveling the Big Questions About God, by Ken Boa.