The absence of Southern members of Congress allowed the Northern Republicans (and Democrats) to act in the economic interests of the North during the Civil War. The main impact of this was to allow the Congress to pass laws that helped to develop the west.
Before the war, the North and South could not agree on developing the west. Of course, the South wanted slavery to be allowed while the North did not. This blocked any real agreement on what to do. With the Southerners out of the way, Congress developed the west. In 1862, it passed three laws that were very important in this. It passed the Pacific Railroad Acts, the Homestead Act, and the Morrill Land Grant Act. These laws helped to build the railroads that brought settlers west. They helped to lure settlers with the promise of cheap land. They helped to create colleges that would help develop new and better agricultural techniques.
By doing these things, the Congress was able to help to open the west to white settlement and economic development.