I'm really not sure why they provided a redundant master cylinder instead of the brake light cable, but I'm sure you can't route it as is. I had a hard enough time getting just the brake line routed. I ordered mine with the bike and it came with the cable and without the extra master cylinder.
As for routing the wire, after I pinched the first one I just did it the ol fashion way with zipties haha. The issue I had was the whole is under where the controls clamp to the bars so you need to route it through a tiny notch in the back of that housing, but you also have to loosen it to fit the wire. I thought I had it set right but when I tightened the controls back down the wire pinched.