When you rebooted, did you use Command + R > Utilities > Terminal to turn off SIP? If not, that is probably why you got the message. If you did boot using that method, double-check your usage, as csrutil disable works.
As to the cloudpaird file, once you have SIP off, you should be able to drag it over from the desktop. When you do, you should be asked to authenticate (inputting your system password).
As to Airdrop not working, that should be the first thing that usually get enabled, once your card is recognized by the Mac (after CAT). If you get Handoff and the other Continuity features working and Airdrop still doesn't work, try signing out and back in on your phone or iPad (along with a reboot). A lot of times that will get it started. If you have done all that, and Airdrop still isn't working, it could be a bug with El Capitan, as several people have had trouble with Airdrop not working even with newer Macs.