I'm not as OCD about where the connectors go, I also try to understand that the SSIS GUI is not intended to be Visio. Other than providing tons of Space between Containers, You can use Sequence Containers (which Can collapse) to organize chunks of logic together. also Like to use the Allignment Tiles from the Layout toolbar to make sure tops/Middles are alligned so the lines are straight. Other than that not much to do it is annoying when its very busy, and every time you open it, the lines are not in the same place.