Hi Mandy,
Here's a fairly complex spec file for a 25km system with 5 entrances:
https://github.com/jarvist/migovecsurveydata/blob/master/migovecsurveydata/sysmig_vrtnarija_extend_spec_2012.dat
But yes, trial and error is order of the day. I think aven will refresh the .3d file automatically (if not, just reload from the 'recent' list in file), so you should be able to have a text editor open on the .spec file, and then a console open to run extend, and then view the new extended .3d.
If I understand your problem correct you should be able to fix this with a single *eswap one station along the branch.