Split pickups would be the easiest way to split the output of the strings like that. However, if you simply want to combine the character of one amps high end and another amps low end, just use a crossover. I believe that's what the guitarist from Tool does. He has a Marshall for his high end and a Diezel (I think) for his lows.
An A-B pedal would allow you to manualy switch between the two, but it would be anything but subtle and seamless. A better approach would be to use a panner pedal (like a volume pedal, but it fades between two outputs) to send your guitars signal to two different amps while you control the mix with your foot. Toe up goes to one amp while your playing on the low strings, and toe down goes to the other amp for the high strings. You would also get the added benefit of all the in-between tones of different mixes of the two.
Another possibility for using just one amp would be to reconfigure a volume pedal to work as a foot controlable tone knob. You could then use your foot to roll off some of the high end (just like a guitars tone knob) when you are playing on the higher strings. This would be very similar to a wah pedal, but it would be a low pass filter and not the distictively honky notch filter of a wah.
There's always more than one way to skin a cat...