Egg chamber in Alien. In SJ ship or beneath it?

While reading the Alan Dean Foster novelization of Alien, Mr Foster makes multiple references that the egg chamber that Kane descends into in the original alien is below the ground level and not actually in the space jockey ship. For the longest time I wondered if the large egg chamber was part of the ship or perhaps a base beneath it. After watching the prometheus trailer for the first time yesterday I have a feeling this question will be answered since the jockey ship and a large underground base with retracting doors are shown. OF course I am assuming that prometheus does in fact take place on what will be known as LV426. What other info is out there which might help to shed light on this? Ultimately what i'm trying to discover is.... was the space jockey ship carrying the eggs as a bomber/terraformer or was the space jockey ship never intended to carry the eggs? Is everything we see in Alien the space jockey ship or are we also seeing a storage base as well? Granted all I have to work on is the novelization by ADF but then again in his version the facehugger had an glazed over eye so I don't know how canon this is. Is there any info form Ridley Scott about this regarding Alien?. Any help is appreciated.