OK, well I believe that it has some excellent features to help you.
1) I would play the score in with click for the passages that need to be regular.
2) I would play the rubato passages without click, but making sure that they fit the picture
3) Move the barlines around until the click fits to the rubato passages
4) Conduct the whole piece through so that you can check that the click is musical.
Of theses, #4 is the most important. I have many colleagues who are good writers, but often have trouble with rits when they record with live players. The reason for this is that the rubato they put in is done by maths and drawing. My clicks often look very complicated, but are actually very musical, and therefore easy to learn for the players. If you make sure that the click is musical you will have little or no problems, no matter how complicated it is.
Feel free to ask any specific questions, as I have done many sessions with live players and click, both for film, TV and for library music.
DG