The design of the system is to report by network, so that they are divided by what goes into a network. The topology of arranging runs with pipes and nodes within a network makes it difficult for us to rearrange them from one network to another.
The reporting is broken out by runs so you have some control at that level to manually arrange them within the excel file.
You can export a network to a VCL file then import it to get a duplicate of the system and then erase the pieces to eliminate duplication. Or simply make two projects to model the two phases.
Other than these ideas it would be a significant amount of work to report them differently.
tim