Have you contacted NewerTech and have they said that they don't plan to support El Capitan?
I haven't upgraded yet because several software manufacturers sent me emails saying that their software was not compatible but they were working on it. Maybe you just need to wait for new drivers from NewerTech? I can't imagine that they are going to discontinue their product line just because Apple updated OS X. I use the original Apple RAID card. I hope that's going to continue to work.
It seems like El Capitan is has really been having a lot of compatibility issues.I would hold off on upgrading util things settle down.