Total Rewire - Trying to understand the process

You don't need any fuses between the solar panels and the controller unless you have three or more parallel strings (NEC). In other words, 6 or more solar panels wired in series/parallel. I might put a fuse between the solar controller and the batteries. I tend to really oversize my wire (1% voltage drop or less) so I don't worry about having fuses everywhere so much. I only have one off the battery. When the solar goes in I might put one between the controller and batteries.