First, sequence structures are generally to be avoided in LabVIEW programming because they disrupt the dataflow paradigm which makes LabVIEW so powerful. That jumping around you see is likely code executing in parallel and making your program more efficient.
A better way to clean up messy diagrams is to create subVIs from sections of code which logically belong together. The wiring between subVIs defines the dataflow and, thus, the behavior of the program. You can select a portion of the code on a block diagram and go to Edit >> Create SubVI. This will create a subVI with all the necessary connectors. You will need to open the new subVI, clean up the panel and diagrams, edit the icon, add documentation and save it. This is much faster than creating a subVI from scratch and then using it to replace code on the messy diagram.
Look at the style guides for other hints.
Lynn