Personally I couldn't get the conjugate plates to work either, and I seem to recall I even watched some pretty long Youtube tutorials and some GPlates tutorials about it. I don't recall what the exact issue was though, so maybe I just didn't use the feature properly (despite my reputation, I'm just messing around with GPlates most of the time, rather than being the all-knowing GPlates Guru).
The easiest way to get the continents to move together is to first just pick up a single continental piece, and decide where you want to start your animation (usually at the date the supercontinent starts breaking apart). In my case, I just picked Central Eocidar, and placed it 200 Mya back at a spot which I thought to be sufficiently far away to reflect 200 million years of movement. I tend to not be too precise with the movements, since you're primarily doing this just to give some basic data and to verify that the idea in your head about the continental movements is actually workable. That's it for this piece of continent: it only has two reconstruction poles: 0 Mya and 200 Mya.
Then you basically pick the next piece, place it accordingly in the supercontinent (in other words, give it a 200 mya pole). Then, decide when it's going to break apart (say, 100 Mya), and simply place it in the exact (or approximate, doesn't have to be 100% precise) same spot within the supercontinent as it was 200 Mya. That's three reconstruction poles: 0, 100 and 200 Mya, and the continent will move with the prior piece until 100 Mya before drifting apart.
Now, if there are shifts in movement or you want the speed of the continent to vary, you'll need more reconstruction poles, but once again I'd recommend keeping it to a minimum. Rememeber that the only real use of a tectonic model is to have an idea where there should be mountains, and in general, give you some geologic data that will be helpful in building the topography. Unless you're building the tectonic model for the sake of having a really amazing tectonic model, you don't need it to be absolutely flawless, just "good enough" will do.
Edit: About those conjugate plates
Now that I thought a bit about conjugate plates, I seem to recall that you needed to add an extra reconstruction pole to the date when the plate drifts apart from it's conjugate. That's because I think it uses the conjugate plate's reconstruction pole while conjugated, if I'm not mistaken, and when no longer conjugate, suddenly jumps to the reconstruction pole of the plate itself. There was some trick to calculating the reconstruction pole of the continent at a particular date, but I've totally forgotten what it was, since I never really used conjugate plates myself.
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