Basically, they were following natural/artificial terrain cues that the Engineers also likely followed or left behind:
- They spotted a massive mountain peak (52,000 feet) that jutted above the clouds, so they used that as their point of entry.
- During descent they detected large "hard spots" in their terrain data that they speculated were likely metal and continued towards it along the mountain valley.
- They then came across some large canyons and entered through an obvious opening. Immediately after, the computer indicated some linear structures on the ground, which caught Holloway's eye ("God does not build in straight lines").
- Following this canyon valley leads them to the large domish/pyramid structures.
Obviously this sequence has been abbreviated for dramatic effect. In reality, they most likely would have spent an hour or two trying to map the planet from high orbit, and, if not, they probably would have circled the planet a few times below the cloud layer to find the most promising landing spot.
But when you watch the sequence, it's not hard to imagine that the Engineers probably also encountered the lone mountain peak jutting through the clouds, decided to enter at that point, and then simply followed the natural contours of the terrain to arrive at their canyon protected building site.
In the grand scheme of things, this sort of "luck" isn't that hard to explain. It's similar to how wildlife pathways form in nature. There aren't signs or surveys or detailed planning by the wildlife. But the characteristics of the terrain encourage certain travel/migration paths.