The Flows pane supports three row ordering modes:
Manual ordering: the rows are ordered by manually dragging them in to appropriate position.
Sorted by name: at each level in the tree, rows are sorted on the name column (case insensitive, and regardless of whether they are group or flow rows).
Sorted by marker: at each level in the tree, rows are sorted on the marker column (see Setting flow markers), and then on the name column (so that the order is predictable when rows have the same marker).
Clicking on a column header toggles between the following three states:
Sorted on this column, in ascending order.
Sorted on this column, in descending order.
Manual ordering