You've pretty much got it right! If you have an insulator that's charged up with a negative charge, and you touch a conductor, the negatively charged excess electrons will move to the conductor until the electrons would rather not move anywhere at all. When this happens, we say that the system has reached equilibrium. If the insulator started with positive charge on it, that means electrons are missing inside of it. The electrons on the conductors will move from the conductors to the insulator. This will leave the whole system a bit positively charged (because charge has to be conserved, and if the insulator was positive and the conductor was neutral, then the end result is that they have to positive at equilibrium).
To address your concern about there being two conductors, because you said they're in contact initially and assuming they're neutral, then yes, they would inherit the same charge as the insulating rod. Since they're of like charges then, they would repel each other.
However, a much more interesting thing happens if you have the balls initially separated. If you charge up one of the metal balls with, say, a negative charge from the rod, the negative charges on this ball will repel the electrons in the other metal ball. This leaves positive charges on the side closest to the negatively charged metal ball. We say that the other metal ball (which is still technically neutral, because it hasn't lost or gained charges, they've just moved around) has been polarized or that we've charged it by induction. Here's a good illustration of what's going on in the spheres:
Because one side of the ball is now positively charged, it's attracted to the negatively charged ball, and they'll move towards each other. However, once the two touch, all bets are off and the electrons move around to equilibrate. This means that both balls will become negatively charged, and then they'll fly apart!
Hope this helps,
MicroMagazine.com. "Investigating FOUPs as a source of ESD-induced electromagnetic interference." http://www.micromagazine.com/archive/02/04/levit.html
(published on 05/04/11)