Hi
The simple trick with the Amiga is to keep your Workbench pretty trim and lean and then just copy it over to your Work partition. That way when you get a problem you can simply format the Workbench and just copy your Workbench back and never have to switch the Amiga off. Saved my life no end of times. I always have more than one drive on computers and have my backup on another drive. I've always got two copies of everything. Probably once a month I copy everything over.
I also have my main Amiga networked to a few PCs so I do copy and burn to CD or stick on a USB. I use ZIP drives and cus the WB is less than 100MB I have my WB backed up onto ZIP.
PS I don't use CF cards, only 2.5", 3.5" and ZIPS. Good thing about a physical drive is that I can stick it in the fridge and hit it with a hammer if it really starts to cause problems. Usually works. I can also hear problems with a drive that goes round and generally tell what I need to do.