What would be the best thing do. I have just talked to Caesar and he asks me to destroy everything in the bunker. I don't want to help Caesar, I’m with the NCR. What would be the best thing to do? Kill, disable Mr. House for Caesar, bring the chip to Mr. House or get the power myself?

Thanks for now.

Depends on whom you want to win the war. Do you support Ceasar, NCR, House or free Vegas? There is no general best option as it all depends on your opinions.
For example, I fought for Mr. House while many other players wanted NCR to win and though of House as an evil dictator.

that's the beef of new vegas. choose whatever side you want to win and join them.

Okay thank you. I want to help the NCR then what to do? And can I help the NCR plus get the power in NV myself?

Someone who can please help? 3 other question. What will happen if I let Benny go and can I do it without they attack me in any way? Are there any reasons to work with Ceaser when I'm with the NCR?

This is a little un topic but I hope you would answer anyway because the quest with the Khans was related to Ceasers camp. How do I get the great Khans to allying with the NCR? The chief don't see that as an option?

"What will happen if I let Benny go" CL will attack you.

"Are there any reasons to work with Ceaser when I'm with the NCR?" Not really.

"How do I get the great Khans to allying with the NCR? The chief don't see that as an option?" You have to complete "Oh My Papa" then talk to Regis.

Okay thank you. I read that you'll have to kill Papa Khan to allying with the NCR? Anyway I have tryed to kill him by placing a C4 on him when he sleeps but when I pickpocket him again it is gone?
I just walk in to his room when he is gone because he doesn’t close the door. I'm really bad at sneak. Could it be because I am "not supposed" to get in the room without a key or what is the problem. Any other ways to kill Papa Khan?

I have killed him now but isn't there another way instead of killing Papa Khan? And when he died a quest named "Can't we just be friends?" failed but I don't seem to have that quest etc. Is it normal that the quest fail?

"I have killed him now but isn't there another way instead of killing Papa Khan?" Nope

About "Why Can't We Be Friends", Papa Khan is a part of that quest, and once you kill him it's a auto fail.