As the good Lieutenant mentioned, the mod you probably mean is my Enclave Improvement Project. And to answer your questions based on EIP's storyline..
When you meet President Eden in Raven Rock, you can ask him why he won't have Colonel Autumn do his dirty work. Eden hints that if you do it, you will have a future in the Enclave. This starts the Joining Enclave quest line.
But for now you must collaborate with the Brotherhood as Colonel Autumn isn't letting you inside the Purifier to poison it. When you enter the Purifier with Lyons and deal with Autumn, start the purifier and poison it. You are knocked out as usual and wake up in Raven Rock. However, then you have the option of joining the Enclave, and if you do, you can return to Raven Rock and start new quests.
In the vanilla game Enclave forces will have small guard posts and vertiberd drops. That's fine if you are their enemy because you must deal with their hostility, but if you join the Enclave then where is the danger if your comrades are everywhere to help you?
For most of the mod the Enclave's field outposts are called off because of the high casualties sustained during the war against Brotherhood. Later on when you have secured the entire Wasteland under Enclave control, you have the option of restoring the Wasteland outposts. Note: OPTION OF.
Does this mod add Brotherhood drop zones everywhere, or is it a single goal to destroy the Citadel?
To destroy the Brotherhood you must conquer the Citadel, Project Purity and Washington Monument. That doesn't simply involve a massacre, but when the conquest is complete Enclave soldiers, initiates, officers and scientists will replace the Brotherhood members complete with daily routines and posters covering the Brotherhood logos. You won't see much real change to the locations, just different guards.
Are the Enclave swell guys or do they treat you like the Outcasts do unmodded?
Because the Enclave have no real dialogue they will greet you simply with a "Hey There" when you talk to them. The few Enclave members that I have made dialogue for treat you as an "associate", a high-ranking associate but without any real military rank.
http://fallout3nexus.com/downloads/file.php?id=12937
Note that because of the major and ambitious nature the mod has its share of bugs, but I work daily to fix these issues. For now I have no major bugs but there are people who seem to have issues with conquering the Citadel.