Any group of galaxies that is gravitationally bound will end up in effect putting the black holes into orbit about each other. The orbits will be across incredible distances and move very slowly, but it will happen. Orbital energy over time gets converted to gravitational waves and thus they spiral inwards. (All orbits actually spiral inwards, it's just the effect is so tiny that in all but extreme cases you won't notice it within the current age of the universe.)

Galaxies which are not gravitationally bound won't encounter each other, so it doesn't end up merging the whole universe into a single black hole.