There are alignment tools for the front and rear covers. If the oil pan is off, you need to align the covers both up and down, as well as side to side. If the pan is still on, then they only need to be aligned side to side. I've never used one for the front cover, as I have an old harmonic balancer that I took a grinder to the inside of so it will fit snuggly, but slip on and off. That's my alignment tool. Since the covers can move side to side, you can have excessive pressure on one side of the seal, and a lack of pressure, causing it to sit incorrectly and leak.
I've never had to align the rear cover, since if it's not leaking, I'm not messing with it lol.