If in an activity like Free Counterpoint the bar line tool is available - it will not be displayed in activities that automatically provide measures.
Bar lines are entered like any other staff symbol and may be placed wherever you like, even "incorrectly."
Bar lines can be dragged left or right with the arrow tool, compressing or expanding their contents proportionally. If measure numbers are being displayed their numbering can also be changed in the bar's "information window" (as with any staff item, select the bar line and press Command-i, or Cntl-i on Windows, to see its information).
Repeat bars are observed by Counterpointer. Use the information window for the repeat bar that ends a section to set the number of performed repeats (the default is 1 repeat).
When you enter a bar line it will automatically connect to any matching bar lines in the staff below, unless you have explicitly asked that this bar line remain unconnected. To request that a bar line be unconnected to others, once again you can turn to the information window for the bar line in question.
When the "auto" button is provided it will automatically enter bar lines for the entire score. It assumes that the first note or rest is the first in a measure unless told otherwise, so if you mean to begin with an incomplete "pickup" measure you should put the first bar line in manually for each staff.