You shouldn't have too much phase cancellation in those two snare tracks (if the snare's heads went completely bonkers out of phase then we wouldn't hear the snare at all) so quit tinkering with numbers and zoom in as much as you can.
The thing you're looking for as far as alignment goes will be the big snappy attack that we're hoping is visible in those tracks. You'll have to be zoomed out just far enough to see the difference in amplitude between attack and decay, but be close enough to know when the two are lined up more or less as best as they're going to get with a reasonable amount of work. For right now all you have to do is line the two up as best as you can. Once you've gotten that part in play through the track, alternating the phase switch in the track settings just to see if before you had the things out of phase, and figure out which has the most constructive interference on the low part of the snare's sound.
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A quick side note, in case you were wondering if the heads should be delayed on disk because there's a slight natural delay between the two in the room. Assuming the temperature in your room is about 21* C (or about 70* F if you don't like Celsius) and you don't have a completely whacked air composition (if you're not in a sealed oxygen room, or the Hindenburg, or on the surface of Venus, this is a no) sound will be traveling at about 771.2 miles an hour. We can put this in slightly more convenient terms - 1129.5 feet per second - and figure out how much delay you'd have in the room if you could separate completely the sound of the two heads. If you're using a six-inch snare (which you are, because six inches is a half of a foot and it makes the arithmetic easier) and you're standing directly over (or under) the snare, that distance of six inches is traveled by the sound in .443 milliseconds:
1129.5 ft/s ^ -1 = .886 milliseconds (sound travels 1 foot in .884 milliseconds)
.886 * 1/2 = .443 milliseconds (six inches is half of a foot, so it takes half of the time for sound to go that far)
If you must use a five-inch snare, the delay is .369 milliseconds.
What's more, this delay gets smaller as you move farther away from directly over or directly under the snare - you can best approximate this by taking the sine of the angle from directly overhead to the center of the drum to the observer, so assuming you're sitting a fair distance away from nutsonthesnare the delay goes down to .384 milliseconds for the six-inch and .320 milliseconds for the five-inch.
So yes, we're talking very small amounts of time, but if you must throw in a delay to complicate things past 'the big lines mean hit and we line them up YAY!' then you have that. Merry Consumermas.
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If you've lined up the attack and tinkered with phase reversal in the host software and you're still not getting things sounding right, post an image of a small part of the wave forms - preferable two to five hits, nothing more. Hopefully we can scribble things back in a paint program and we'll make sense of that.
Jeff