I assume the terms "top 6" and "top 8" refer to the number of placing positions for double elimination ladders.  The number of placing positions determines the structure of the double elimination bracket.  The answer depends on if your match numbers are numeric only (e.g. 1, 25, 100) or use letters and numbers (e.g. "AA2", "AD19", "BC62").  This is specified in the "File" menu's "Ladder/Misc. preferences..." window.

If match numbers use letters and numbers, you can use the "View" menu's "Emergency bracket repair..." feature to update the placing for each bracket (one by one).

If match numbers are numeric only, you can't change the placing positions once the tournament starts.  However, TournamentSR saves a backup copy of the tournament just before [Start the tournament] was clicked.  The backup copy uses the extension "AtStart" (instead of the normal "xml").  In this case, you'd launch another copy of TournamentSR (on the same computer is OK), load the AtStart file, modify the placing positions for each bracket (one by one), then [Start the tournament] and enter in all the results.  At that point, you'd stop using the original TournamentSR instance and start using the second one.

See the Reference Manual for information on Emergency bracket repair and the AtStart file.