The biggest challenge could end up being matching the output volume of the P90's with the Jag pickup. If the P90's are much louder than the Jag pup, one simple fix could be raising the Jag pup closer to the strings, and the lowering the P90's to try to balance the outputs. Of course, this affects the way each pup will sound, and it will not necessarily end up with each pup in their sweet spot.
There are some basic principles of the parts in a typical guitar circuit that are helpful to know. A higher number pot will sound brighter than a lower number (volume & tone). So, a 500k ohm pot will sound brighter than 250k ohm pot. 500k pots are typically used for tone and volume with humbucker guitars. 250K pots are typical (volume & tone) in an SSS Strat. If you wire an SSS Strat with 500k pots, it will sound overly bright, and harsh. You'd have to roll off the tone and volume knobs a lot to tame it.
SSH wiring typically uses a combination of 250k and 500k pots as a compromise. I'm not familiar with Jaguar guitars, but it looks like Fender uses 1 meg pots which will make pups sound bright. Assuming this guitar will be 5 way switch, volume, tone, tone, perhaps, a good compromise for pot values would be 1 meg volume, 500k tone, 1 meg tone. But, I imagine those P90 pups are going to sound very bright with a 1meg volume pot maxed. Maybe, 500k volume, 1 meg tone, 500k tone would be better.
You can effectively reduce the value of a pot with a resister, or resisters. As an example, if you have a 500k pot and you solder a 750k resister in parallel, it will essentially make the pot operate as if it's a 300k pot, and the guitar pickup will sound darker. This particularly helpful when you've already wired a guitar which sounds overly bright and you want to tame it. I have one guitar that ended up too bright after wiring (with volume and tone maxed). I just roll off the volume and tone knobs.
The capacitors in a guitar circuit act as frequency filters, reducing high frequencies. A higher value (ex: .047 uF) will filter more highs, sounding darker, while a lower number (ex: .022 uF) will filter less highs.
Perhaps, the best strategy would be to wire for the typical pot and cap values based on P90 pickups, and let the chips fall where they may with the Jag pup in the middle. Anything else is likely to compromise the resulting sounds of all the pups. Of course, the Jag pup probably will not sound quite like a Jag pup without those bright pots. But, after all, it's in the middle position, which often gets skipped over by many players.