i'm about to build my first bass and it'll have pj bass pickups and i was wondering how to drill the body so the wiring doesn't show between the pickups and the bridge, because the pickguard won't cover both pickups.
I think the hole for the bridge pickup wires is made with a long drill
through the same hole that serves the output jack.

The routed slot for the precision pickup wires will be covered by the pickguard.

I'm only guessing here.
Get confirmation from someone who has actually done this.
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SYK's right, you need along drill bit for the pickup that the pickguard won't cover. For the one under the pickguard, you can just route a channel like you would find under a normal pickguard.