Are you trying Nisus Writer Express or Nisus Writer Pro? If you’ve got the former, it doesn’t surprise me that it didn’t work. But in NWP, don’t try to sort it out manually; before you do anything, go straight to Styles view and set up each stream.
[attachment=0]Screenshot 2020-10-26 at 21.59.09.png[/attachment]
N.B. I have my stylesheet set up to use markers which are 2 pts smaller than the text size but raised 2 pts—you can see the effect in the screenshot. I find the superscripted markers so small they almost become invisible, and this way they are a better size without affecting the line-spacing.
PM me if you think I can help you more. The forum community is very helpful, as is Martin of Nisus, as KB will attest, I’m sure.
Mark