Regardless of what people say, you really don't have to worry very much about this. All you need to do is make sure that the caps are installed in the correct direction so that they mate up properly to the housing (if they are asymetirical, some axles are, others are not), and that when tightened down, they create enough clamping force to keep the carrier bearing race from spinning, without being so tight that they deflect the race (crush it into an oval instead of a circle - this will ruin the carrier bearings). If they can function and serve that purpose, you are good to go, regardless of if they are in their original location or not.
To test fit the caps, do the following:
First, put the new races in, point the caps in the necessary direction so that they mate properly with the housing and case, and check the clearances by hand. Spin the cap bolts down hand tight and see if you can spin the race in the journal or if there is any play between the race and the cap (there should not be - if there is, the caps are either on wrong, you are using the wrong races, or a bearing has spun in the housing).
Next, take the cap bolts out and test for "rock" in the cap. Put your thumb over one bolt hole, and your index finger over the other, and try to rock the cap back and forth around the bearing race. You should not be able to move the cap any appreciable amount - if you can, the caps are probably on backwards, there is a problem with the bearing surface on the housing, or you are using the wrong races. If this happens, switch the caps and start over.
Personally, when I build an axle, I will sand the faces of the main caps down ever so slightly on a belt sander, to create a very small amount of "rock" on both caps- this puts the races under tension and ensures that they cannot spin in the housing journals under extreme use. If you do this, make sure you sand with a fine belt and in VERY small increments. You DO NOT want to create excess tension to the point of deflecting the race, otherwise you will destroy the carrier bearings. It is also very important to keep the mating surface of the caps flat.
Alternately, some axle builders will "dimple" the surface of the journals on either the axle, the caps, or both with a prick punch. This deflects the metal, creating "high spots" which serve the same purpose (Both accomplish the same thing - creating adequate clamping force to keep the carrier race from spinning in the housing) .
The point I'm making is that it isn't the end of the world if you think you have the caps mixed up. Just test the fit, and as long as the caps are pointed in the correct direction (if they are asymetrical), and clamp down adequately on the carrier bearing races to keep them from spinning, but do not have excess "rock" to the point of deflecting (crushing) the bearing race, you are pretty much good to go.
-Hans
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