You could use either, but if you want to use deep sleep and immediate response as soon the alert gets triggered, you may want to go for active high on WKP.
@RWB, the ALERT output is an ACTIVE output meaning it goes HIGH and LOW without the need for a pull-up or pull-down. You can, however, put a week pull-down just to be sure the pin is low on power-up. To do that you would need a resistor from the IRQ output to GND (use 100K). The IRQ also goes to the WKP pin of the Photon. The way you have it shown, CAP_ALERT is basically shorted to 3V3!!
@RWB, you need to look at the Adafruit schematics again. The way you have it, CAP_ALERT is connected to 3.3V instead of the junction of the IRQ pin and the 10K pull-up resistor!
I suggest you take a look at Section 4.6 of the CAP1188 specs which describes how the IRQ pin can be setup. With the pull-up, I suggest you use active LOW for the pin.
@RWB, your active low schematic is still wrong since you are shorting the IRQ line to 3V3!!! The schematic is like the high one except that the resistor goes to 3V3 instead of GND. I suggest you use the active HIGH since CAP_ALERT will be held low even when power is off .