Your post/question is a little confusing. Does your cruise start in Kotor and you will get there on your own? In that case, the Budva bus station, plenty of departures daily and worth to get there early as Kotor is beautiful.
If you start in Budva, I would think by the harbor. You would have to call the company on where you will start
As Alex says the most likely spot is the bus station near the stari grad
You dont happen to remeber which company you went with just hearing some negative things about some of the companies
I have not heard about bad companies.
In Budva you can find plenty of travel angencies that offer tours. Someone on this board mentioned about cruises between Budva and Dubrovnik which I was not aware off, but that would be amazing as the coastline is just stunning. I am sure a touragency can you advice on that