Just checked out the template myself. Photoshop tells me that "Some text layers might need to be updated before they can be used for vector based output." I think that it's probably due to different versions of Photoshop, though I thought older versions used vectors for text layers too. Weird.
Updating the text layers (which is necessary in order to edit them) causes some layout changes.
(Edit: given the rather stringent layout of *A* and *B* things, this might be a bit annoying to fix.
)
Looking through the template...
Why are there layers for *A* and *B*? For example, there are two Card Cost layers but they look about the same. (Note: I figured it out later on in this post...)
For the Potion cost, the "covers" for various card types seems like a clunky way to do it. The easier way would be to have a single layer with the blank coin background, and have each card type background have those "covers" by default. So most of the time, you would just turn on the coin background layer for your cost, but you would switch it with the Potion image if the card cost Potion.
Hmm... looking at the card type templates themselves, I see that some are marked *A* and some *B*. I get it. Weird that those different templates are shifted like that. With this knowledge, I would recommend reorganizing all the *A* and *B* layers elsewhere in the file. Right now, you have it organized like this:
Base Card Text (group -- you call them "sets" in your guide)
- *A* Card Cost
- *B* Card Cost
- *A* Card Type Line
- *B* Card Type Line
But it would be easier to use if it were like this:
Base Card Text (group)
- *A* layers (sub-group)
-- *A* Card Cost
-- *A* Card Type Line
- *B* layers (sub-group)
-- *B* Card Cost
-- *B* Card Type Line
This way, you can turn on or off all the relevant layers at once instead of having to go through and change the visibility of each one.
I hope you get what I mean. When I have some time in the future and/or I want to make a new card image, I'll go about messing with the organization to suit my own use.
Also, the multiple text layers for the card text that just have different formatting... it might be excessive, especially because some cards might need custom formatting anyway. But I haven't really looked carefully at what you provided; it might be handy in general.
In the "Finishing Up" section of your guide, you instruct using "Save As". If you are saving as an image, my understanding is that it's better to use "Save for Web & Devices". Also, instead of flattening the image, I recommend just copying everything into a new file:
Ctrl+A (select the entire canvas)
Ctrl+Shift+C (merged copy)
Ctrl+N (new file, which should have dimensions already adjusted)
Ctrl+V (paste, which should by default go into a new layer)
The new layer will preserve transparency and you don't have to worry about accidentally saving over the original file after you've flattened out all the layers.