Old question,m I'm finally getting around to:

OK, I have two lights, two switches, both lights are on the same fuse. It
looks like both junction boxes have other circuits running off them, which I
think is the same fuse.

Plan is to run three way wire between the two lights white/red to socket,
blacks connected. Then run two way wire to the 1st switch white (black tape)
to red (socket) black to black. Then run three way wire bewtween the two 3
way switches (white wire taped).

But I'm not sure if it matters which socket I run the switch to, since they
both have other circuits running off them. Can't I just run my other
circuits off the black/white in either junction box as it is now? This is
where it gets a little confusing.

TIA