If you’re not happy with the order of the matches you can adjust it manually. Go to Run Tournament and click Change match sequence, times, fields, placements.
Under Modify you can youse the hand symbol to pick a match and move it to a different place. The rest of the matches will shift automatically.
An appearing yellow frame means that one team is supposed to play twice at the same time.
By clicking Save or Save and Return you can save your settings.