My patchoo has been running pretty well, I've been keeping up with the updated patchoo.sh changes - and pretty much left well enough alone. With 10.10.4, I was watching my patchoo pretty closely, it doesn't seem to be prompting for system updates.
Now I'm trying to figure out why.. I saw this Deploying Apple Software Updates but I don't know if that is something I need as it says it's optional. Further, I have the JSS set my different software update servers by IP ranges. I'm a little confused as it talks about using Respado (whatever that is) but I just use our internal SUS based off Server.app.