You follow the original path as closely as possible.
Check the original wiring with a multimeter before going to that effort. You can get cheap ones.
Consider professional assistance if this seems too difficult.
The speaker wiring won't go through a fuse box.
You can go straight from the headunit to the speaker. It is far easier to check for continuity using a multimeter.
Don't rule out a headunit fault either. If it is aftermarket, check for dodgy wiring.
Regardless of chassis, eg. the Hilux dual cab SR5 to SR. The SR5 has full rear speaker wiring and the SR is missing it from the front kick panel to the headunit.
The hardest bit is getting the rear subframe bush out and back in/lined up. Use a screwdriver if you don't have a roll pin/podger bar through the hole.