Thanks for your email.
If you are not pumping more water to the Clarisea than it can handle (5000 l/hr for the SK 5000 and 3000l/hr for the SK3000) , you should be able to shut the bypass and not worry about waste to the skimmer.
Keeping the bypass open may lead to an alarm especially when you install a fresh clean roll as the fleece will be clean along its run though the Clarisea and it will take longer for the float to actuate as the fleece will take longer to become dirty and operate the float for the first time after the fleece change.
Once the fleece is dirty you can open the bypass again if you wish as it will only be the small section of fleece at the top of the Clarisea that will be rolled on each time meaning the float will actuate more often and wont trigger the 8 hour alarm which may happen with a new fresh fleece if the bypass is open.
Remember that when you change the fleece pull the power pack of the Clarisea from the wall and wait until the controller lights go off and plug back in, this will reset the controller and give 24 hours before a float alarm to allow a new fleece that’s installed to become dirty, once there is a float actuation within that 24 hours the controller will then reduce the alarm time to 8 hours between float actuations before alarming as it will then know the fresh fleece is dirty and should then be running normally.
We suggest mounting the Clarisea before the skimmer as any detritus that the Clarisea pulls out will be removed from the system completely , any dissolved organic proteinaceous compounds that don’t get caught will then be removed by protein skimming. It is far more efficient to pull detritus out mechanically with the Clarisea than for it to degrade to a point that the skimmer has to try and pull it out.
Running a Clarisea should help reduce nutrient levels within the aquarium as the waste wont get chance to degrade within the water column in the first instance as it would with using submerged socks or protein skimming alone.
Hope this helps Tony