The necropolis ships spawn in the zone that have a skull on them on the World or Continental map. There may be one or more of them in the zone. I'm not yet sure if they always spawn in the same spots but go around the map and watch the sky - they stand out and will shoot out 'shadow bolts' to nearby summoning circles.
The summoning circles are always nearby and the active ones can be found by watching the 'shadow bolt' animation that shoots from the necropolis ship. Follow the direction of the 'shadow bolt' to the summoning circle and kills the mobs in that area. If you do not see the shadow bolt shooting from the necropolis ship to a summoning circle, it means other players have already stopped the ritual and that area is no longer active. They have a high chance of dropping a Necrotic Rune - I got one about every 2 or 3 mobs.
Every so often (I was there for about 5 minutes before it happened), 4 mobs appear around the crystal in the summoning circle and speaking with them allows you to use 8 of the Necrotic Runes to stop the ritual. Once you do that, they spawn into a Shadow of Doom which needs to be killed for a quest. There was over ten people at our summoning circle and we just aoe'ed them down but with decent gear and being smart I bet they could be soloed. They can be feared, stunned, snared, etc so do what you can. Also when you summon the Shadow of Doom, attack it right away to prevent others from tapping it.
Hope that helps to anyone who is a bit lost for this quest.