You can find what step and where to go to complete the next step in the storyline by looking at your current missions. The companions' missions to go someplace besides a cantina or ship show up here under a "Companion" category.
To see if they want to meet at a rest area or your ship, get them out and look at their portrait. If you see a yellow ship or person icon, then they want to talk to you at your ship or a rest area.
Torhead.com has a list of all the companion missions here:
Jedi Knight: http://www.torhead.com/missions/catg/8/subcatg/5
In my mission log I see no "Companion" category. I see that Doc wishes to speak with me on my ship but this is a recent event.
Kira shows no Icon of the sort when I summon her, but, unless memory fails, I was supposed to go with her to some planet and help some people there. I'm pretty sure that at the time it was too hard for me and I didn't do it. Still, I could be mistaken.
Is there always a Companion category "slot, or whatever it's called" when I pull up my log, or only when they actually have a mission to do with me?
Thank so much for your help!