First of all at the beginning of the movie the 'engineer' is wearing a robe rather than the suit as seen in all other engineers. This may lead to the rise that there are 2 beliefs of these engineers. Much like there are multiple religions here on earth. These 2 beliefs (based on the actions of the engineers) are that
1. The Human-loving engineers believe that human are made for a purpose and a reason which is what the team is hoping to find out. This would explain why the beginning engineer was clearly sacrificing himself using the "black liquid" to make human DNA. This would also explain the change in clothing. (robes rather than equipment looking suits). 900
The ship in the background also is different to the on seen in the movie. Possibly a personal carrier used only for transport and as seen in the behind the scenes picture of the elder engineers it is possible that the younger healthier engineers are sacrificed.
2. On the other side the Human-hating engineers believe that the humans are a failed science experiment and should be destroyed for further experimentation. The change in clothes from robes (usually associated with the church) to the military looking equipment It gives rise to the idea that the engineers on the C-Shaped ship are military personal seeking out the UFO shaped ship to destroy the human life they are creating. It is also most likely the "black liquid" seen on this ship is a variation of the one seen at the beginning of the movie. It appears to be a bio-weapon to alter the DNA to create a super-being strengthening the host DNA. The dead (possibly soldier) engineers on this ship were most likely contaminated with the bio-weapon liquid and were self eliminated. However there is a possibility that these suits are merely space suits but is unlikely due to the fact that at the beginning and end that an engineer goes outside without wearing a mask seen by all other suits.
Concluding i believe because of what i saw represented in the movie that there is a war going on between the engineers. Which isn't hard to believe considering all the war and violence on earth however this seems to be a more technologically advanced war being fought on different planets such as LV-223 (Prometheus) and possibly LV-426 (alien). 900