To offer an actual answer to the question instead of a string of comments, I would start with just one or the other mic, get what you like out of it, then add the second. My choice is the D6 at the soundhole of the cajon, because that will give you the fundamental bass "thump" of the thing, as well as a decent amount of the snares, tambourine or other internal janglies that your particular instrument has suspended in it. Play with this mic's position and relative angle to the port. You don't want the disphragm of the mic at or too close to the actual level of the port, because the turbulence produced by the interaction of the air inside and outside the drum at this point will cause issues. A few inches outside the port and pointed directly at it will typically get you the best "boom"; a few inches inside will de-emphasize the bassy nature of the drum in favor of the impact and the internals.
Once you have the sound you like there, if it fits the mix, then forget the i5. However, if you want more of the "slap" of hand on wood than you get from behind the drum, then place your i5 pointed at this area of contact. Now the fun begins; you need to make sure the i5 isn't cancelling out anything you want from the D6, by very carefully moving the i5 to position it so that the fundamental frequency it's getting is "in-phase" with the D6's. The easiest way to do this is to give direction to a stage hand while you yourself PFL these two channels. As the assistant moves the mike directly toward or away from the box, you'll hear different frequencies get louder or softer. It doesn't take much.
Depending on the mic placement and the drum structure, you might be able to get enough access to measure and adjust the relative distances. Take a piece of string, and go inside the cajon, to the center of the front panel (the tapa) at about the height from the base at which the player normally strikes it (if he hits all over, find the geometric center). Hold the string against the tapa with one hand, while pulling it taut with the other, out to the microphone head. Mark the point at which the string touches the head, then keeping hold of both points on the string, move out in front of the cajon and stretch the string from the same point on the front of the tapa out toward the i5 (don't change your hold on the other end to adjust length). The string should just barely graze the i5's grille; have someone else move the mic in or out from the tapa until it's at the right distance and out of the way of the drummer's hands. Then, because the D6 is exactly the same distance behind the tapa as the i5 is in front of it, these two mics will be perfectly out of phase, so you'll need to invert polarity on one or the other so the signals combine correctly.
If this is a dedicated recording session, and you're not also playing for an audience, then you have control over the space and what else is in it. If you like the way the cajon sounds naturally in your space, then don't close-mic it, room-mic it; set up one or two small-diaphragm condensers at a distance from the instrument such that you get a good overall mix of the instrument itself and the surrounding room. These kinds of instruments get recorded in everything from vocal booths to bathrooms.
Mic placement is an art in itself. There's math, to be sure, just like there's math behind the perspective in a painting, but there are also so many variables that it's impractical to try to calculate the ideal microphone selection and placement. The best thing to do is experiment until you find something that works.
