You got a good price on the eheim filter,nice..........
You can clean it by soaking it in vinegar and water for a little while,then scrub it real good,to get the inside more difficult areas I would suggest a stiff bristle bottle brush.
Or, you can soak it in bleach water,scrub it real good,then soak it in water saturated with a good de-chlorinator (4X's the amount of recommend dose of de-chlorinator to neutralise the bleach)
Once it's cleaned up,put it on the aquarium,fill it up and turn it on.Add filter media,put a small amount of your aquarium gravel in the bottom of the filter housing,just behind the media and let it run. Let it run for a while,with the 'bubble filter' running also(more than a couple of weeks) to seed the new filter with bacteria.You can use it in conjuntion with the bubble filter,or you can remove the bubble filter.
Now,the fish...........
Change the water and give them plenty of clean water daily,clean the gravel to remove wastes.Put the effected fish in quarantine (if available),it will help reduce the chances of the other fish bullying him/her and increase the chances of recovery.This should be enough to cure the fin rot,if not.......
Before adding medications,remove any carbon from your filter.Maracin+ is an anti-fungal,and would be my 1st choice of treatment (I didn't notice a brand you were using,so I thought I would give you an option) Kenacyn (Kenamiacyn) is also a good choice. After the fin rot is cleared,you can treat with Melafix to prevent re-infection and speed fin re-growth.Melafix is not a disease treatment medicine (often misunderstood) it is an antiseptic for prevention of infections,not a treatment medication.AFter treatment and fin rot is cleared,change the water 50% and add carbon to remove the remaining meds from the water.
Good luck and I hope your fish gets better,
Welcome to Fishlore.............
