I’m sorry but I don’t quite follow what you are saying, however:
The current versions of the program (V1.4.x) should be able to open any SOTA CSV or TSV format that I know of without any mix-up of columns.
If you open the program and then press F9 you should see several boxes:
into which you can enter ‘Callsigns’, ‘Bands’ and ‘Modes’ the program will quietly accept almost anything you care to enter in three boxes, just be sure to press enter after each Call / Band or Mode (including the last one) in the lists.
Remember to click Save at the bottom.