Yes! Ensemble Thunderbolt is fully compatible with Mac OS X El Capitan (10.11 to current). Please be sure to download and install the latest El Capitan compatible software package for your product from Apogee's site.
Although Ensemble FireWire is not "officially supported" after OS X 10.10.5, it is still compatible with OS X 10.11 and should work just like it did on OS X 10.10. You can download the latest installer for Ensemble Firewire and use it on 10.11 even though it says "Mac OS X 10.10 and 10.9 only".