I have one Sun Titan card. If I try to put more than one Sun Titan into a deck, the site helpfully tells me I don't have enough Sun Titans, and lists the extra card as one I'll need to buy. However, I can make any number of decks featuring my one Sun Titan, and the site does not have a problem with that, and, in fact, doesn't seem to be able to notice it is happening.
I can see how this is a good feature for some, as in real life I could build any number of decks around my Sun Titan, although they couldn't all exist at once. However, IRL I share my collection with my girlfriend, and we play with others without large collections, so our decks all coexist. I like to have a large number of decks, and I find it to be a fun challenge to create a deck using the leftover "trash" cards we don't use for our main decks.
In the example of the Sun Titan, it's easy to keep track of just the one card (and a good card like that will probably have a deck built around it anyway). But for cards like Pacifism, which I tend to put into every white deck I make, I have 13 copies, and keeping track of how many are already in "use" can be tricky.
Is there any way we can have an option to have the site track how many of our cards are "tied up" in decks, to prevent us from overbooking cards?