Just found my answer, looks like the answer is "sort of"
Quote:
IGN: Can we start our online league with a fantasy draft?
Ferwerda and Castorani: Yes, we created something this year called a profile draft. Essentially, on your machine, you'll pre-rank the entire list of NFL players and what round you'd like to draft them in. This is very similar to a fantasy football draft pre-rank system. Once your profile is set, the league will automatically run the draft and assign your players based on your preferences.
This is our first iteration of a draft, and we'll be looking to expand to a real-time experience in the future. However, this year, we decided it would be best to focus on the base experience and expand as we interact with our community and build features that everyone wants.
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IGN: Madden NFL 09: First Online Leagues Details