Im on the part where you try to negotiate with the NCR (last part of quest near the train station being attacked by ncr troops with pacer) and I want to be on good terms with the ncr. What should I do? If i kill off the ncr can i still get my rep to idolized later on? I want to be on good terms with the kings too so i can get the rewards.

It all depends on how you handled things with The King. If you failed to tell him that the NCR had sent an emissary to discuss relief efforts but that the emissary had been beaten up, The King orders you to wipe out the NCR. You'll have to either kill them or all of The Kings. If you did mention the emissary, you can resolve the whole quest peacefully.

If you do kill the NCR, you will never be Idolized by them.

spoilers all up in this [censored]...

also

Sorry, I just noticed what forum this is in - I've sent a request to have it moved. Also, check your spoiler tags.