Are we allowed to put the two 8.5 x 11 inch sheets of paper in sheet protectors?

Yes, the two 8.5 x 11 inch sheets of paper may be in sheet protectors. Remember that you may only have 2 pieces of paper.

Does one of the 2 sheets include the national list or not?

Yes, if the team chooses to include the National Tree List or any parts of the list in their notes, it must be included in the two 8.5" x 11" two-sided pages of information. This is a new rule for this year.

For the competition I was not clear about the commercially published resources. Could these be the Audubon Field Guides, or any other Tree Guide?

Yes, any commercially published resource is allowed.