Very cool.
I have some layout ideas/feedback.
I would change that serif font to sans-serif one like Verdana or Arial. It would improve readability a lot.
I think there should be more than 3 elements in one row. There's enough space for that and there would be less vertical scrolling. You might be able to fit 6 elements in one row if you wanted.
Usability-wise, I think that the main issue (for me at least) is that unupped and upped versions are not next to each other. I would list the cards so that you have upped version under unupped one, followed by a line break. Like this:
(0) Aether Pillar
(0) Aether Tower
(0) Spark
(0) Ball Lightning
etc.
I see that the deck image is done using Planplan's code and the image is hotlinked from his server space. I don't know if you guys have talked about that, but if not, I would ask for a permission to do that. Also I think that whether or not permission was given, credit should be given for using the Deck Image builder.
That's all the feedback I could think of. Take it or leave it.
I think that the tool is very useful and easy to use. It will be a great addition to the upcoming Tools section. Good job.