Many children's parents in my family tree were never married. How do you put down the mom and dad and show they were never married? This always gets me in trouble because people say, "We were never married."
On paper you can use the traditional relationship indicators, also known as a genogram.
Here is range of genogram symbols from Wikipedia.
If you are using a family tree software, you would still enter the pair as a couple for the software's sake. You should then be able to edit the 'marriage' details to be more specific to each person's case. Eg Divorced/ never married/ engaged/living together etc. It is a bit more time consuming, but it can be done.
I haven't tested myself how the software then shows them in a visual tree format but I do know in pedigree lists etc. it has this information attached to each individual.