On tab "Presentation" in the Excel Import settings there is a section "Layout" with a single "Layout" settings. This setting specifies which layout algorithm to use for arranging your diagram right after import. For flowcharts, "Hierarchical" is a good choice.
Aside from that you can use an additional column with a group ID to put nodes that belong together into a shared group node.
Another approach would be adding columns for x and y position and mapping the corresponding values to node positions using the properties mapper.