Mine is a 90 Accord, but I just read the timing belt instructions for yours and this part seems to be the same. I just finished replacing the timing belt, balance shafts belt, and water pump. I, too, had a little difficulty figuring out the rear shaft alignment. Like what you said, I noticed a recessed dot in one place, and a v notch on the outer edge, but no clear places to line these up with. For mine, to align the rear shaft, you have to find an access hole behind the rear balance shaft (you have to remove a bolt to use it). You align the shaft by putting a bolt or screwdriver or something in it (they recommend using a 6mm x 100 mm bolt, inserted a minimum of 74mm). Supposedly, the bolt/screwdriver/whatever will only fit when shaft is in the correct alignment. My Haynes for 90-93 Accords went through this, I'm surprised that 94-97 didn't.

It still didn't work out exactly as it should have for me. I kept slowly turning the rear shaft sprocket, and found that I could fit the bolt in in more than one place, which didn't seem right. I ended up noticing that there were (really faded) two red paint spots where someone had marked the sprocket position to the area just next to it, which also happened to be one of the spots the bolt fit - so that's what I used. But without the red marks, I don't know how I would have been able to determine which of the several positions that the bolt would fit in the access hole to use. I just finished this yesterday, and the car runs fine (no excess vibrations, which I assume would be the case if the rear balance shaft was out of alignment with the engine).

So, I would recommend reading the timing belt instructions, which are located in the FAQ sticky post in the Accord and TSX forum. If you encounter the same thing as me, that the bolt fits in several positions instead of just one, look carefully for any paint or other marks made. Hope that helps.