This part. It's kind of confusing at first, until you realize that the antique isn't coloring the leather, it's just sitting in the tooling to highlight it. Since your antique should always be darker than your dye colors, it doesn't matter what color it's sitting on top of.
Here are the basic steps with ANY finish when using it as a resist.
1.) dye entire piece
2.) resist entire piece
3.) antique the spots you want antiqued. Really rub it in so it fills your tooling nicely.
4.) apply the same finish you used as a resist over the entire piece CAREFULLY (spray if possible). At this point you run the risk of pulling your antique out. The biggest purpose for this final layer of finish is to seal the antique into the tooling.
Now, you may be wondering why you resist the entire piece if you may not be antiquing the whole thing. If you only apply your resist to the portion being antiqued, then you're going to have an uneven looking finish after step 4 because there will be less finish on the non-antiqued portion. Also, I don't have any experience with Wyo Sheen, but I know ClearLac and Resolene really need to be thinned in order to apply it properly without smears or buildup that will crack in the future. Put it on in a couple of thin layers before trying to antique, then do the same when you apply the final finish.