Well, I don't think I disabled SIP but I'm not sure where that is done in the guides that I've been following? I know how to disable SIP in a real Mac; is the process different in building a Hackintosh?
EDIT: From what i read you do it via editing your Config file. From a booting system (El Cap), would I?
1) Open Clover, Mount EFI
2) Copy and add lines of code to the config.plist - Does where matter?
<key>RtVariables</key>
<dict>
<key>CsrActiveConfig</key>
<string>0x3</string>
<key>BooterConfig</key>
<string>0x28</string>
</dict>