Keep in mind that the smallest over current protection most likely will open (blow) first regardless of position in the circuit. These fuses, (7.5amps max), were positioned between the Block Power controllers and the tracks on the power side of the circuit. Commons are complete back to a common bar and the common side of the two transformers.
Fuse blocks. From the Grainger website. Click on the underlined phrase to access.
I use Polyfuses, but not for this application. I use the 3A ones between pickups on passenger cars or between the tender and locomotive to protect the wiring. They open too slowly for me to trust them for protecting electronics.