I have a recovery partition but OS X doesn't use it for recovery
If can not boot to your recovery partition, there are two alternate ways to enable/disable SIP. 


Create a USB flash drive installer. You can plug the flash drive
into the USB port and restart with the alt/option key held down. To
create the flash drive, you will need to download El Capitan from
the App Store. You do not reinstall El Capitan. Instead you use
the instruction given here to create the flash drive.
The other alternative would be to install rEFInd. During
booting you can select to enable/disable SIP. You would not have to
actually install rEFInd to your internal disk. You can install rEFInd
to a flash drive as well. See here for more information.


The advantage to the first method is the flash drive completely replaces your Recovery Partition. In other words, everything you can do once booted from the internal recovery partition will be available when booted from the flash drive. Of course, this requires downloading all of El Capitan which is several Gigabytes in size. If you have a slow internet connection speed, then the second method, involving installing rEFInd to a flash drive, would be a more favorable option.