It's never quite as simple as at least I thought at first, because the controls all interact with each other. I hope this isn't egg sucking advice, but the trap I've fallen into is to think is thinking that because I draw it all in a neat row from left to right the signal will go like that. Well it will, but it will also go backwards and round the houses, because the signals aren't electronically separated. So although you have individual tone controls on each pickup, in fact all the tone controls affect all the pickups to a greater or lesser amount, and the volume settings can also affect the tone. This makes my head hurt so much trying to figure it out I've given up and just have one tone control on my guitars!

Thus the order you have things in makes a big difference. If things are in the order pickup -> vol -> tone -> switch then each tone control affects the sound on all pickups while its switch is on, even if the volume on that pickup is turned down to 0. If you have order pickup -> tone -> vol -> switch then the tone control won't affect the other pickups when it's volume is 0, but still will as the volume is turned up.

Practically speaking the takeaway is that you can't have a big treble cut on one pickup and full treble from another. How much this is an issue is down to you. It hurts my sense of order, but great guitarists have been getting great sound out of guitars with multiple tone controls since they were invented without giving a damn about how the knobs interact, just twiddling until the sound was right. It gets even worse if you throw phase and coil tap in the mix.

At the moment I've gone off complex multi switch wiring a bit. Too many of the combinations didn't seem to offer much. I suppose in an ideal world I'd build a new guitar with a temporary setup so I could try every possible combination, then simplify it so only the good ones were left, but I'm not disciplined enough or for that matter enthusiastic enough about soldering...