You *should have 3 fuses, one at each power source. The panel, the controller, and the batteries. Each fuse ~25% bigger then the expected max for charging, but not oversize for the wiring. The panel fuse should be at rated output + 25%, the other two fuses should be panel WATTAGE /10, +25%. As long as the fuses aren't to big for the wiring, that covers all charge controllers - mppt and shunt. Did I mention do not use fuses to large for the wires? Put the fuses as close as reasonable possible to the power sources.