Hi,
no you can participate in both, but the tracks have a different focus.
- in the pre-made deck playing track your agent needs to be able to play multiple decks (see the website for a list), but will only face opponents playing one of those three decks
- in the user-created deck playing track you need to provide an agent and a deck. the agent can be optimized for playing this single deck, but can face an opponent with any other user-created deck as well.
Depending on the used method those differences can be important, but if your agent is suitable for playing against every possible opponent you can simply submit to both track. Just also provide the deck you want to play using the usual deck building constraints set by Blizzard.
Best,
Alex