Well the order you put them in the file doesn't really matter, if that's what you're asking. I usually do my files with the default group at the top and then going up the inheritance tree til I get to Owner at the end. But that's just me; it really doesn't make a difference.
The rank values you give them is what determines how they rank up if you use /pex promote; ranks with bigger numbers are less important than ranks with lower numbers and rank '1' is the most important rank you can have. So promote will rank them up from the highest number down to the lowest.
If you're using /pex user <username> set group <groupname> though, then you don't even need to use rank values because you're just putting people directly into the group you want them in.
Oh those. There's no required order to those either, except that if you're going to use any negated perms, it works better if you put them before the other nodes. This is because if you have a node with a wildcard on it, like essentials.* , you can't then subtract permissions from that after you've given it. You need to negate perms first and give the * perms last. Other than that one thing, the rest is random.
Comments on Profile Post by NLGuillermo