Federal courts have limited jurisdiction, so the district court must have found some "federal question" allowing the trial to proceed there rather than in the state court, as there shouldn't be any diversity jurisdiction as, one would believe, both the parents and the school district should be in Pennsylvania.
Any verdict or final (appealable) decision by the district court judge would then go to the Third Circuit Court of Appeals. Usually, an appeals panel consists of three judges. Occasionally, however, the Court of Appeal will follow that up with an "en banc" hearing, in which, essentially, all judges of the Court of Appeal hear argument and reach a decision (usually with a significant dissent) on an issue.
After any such alppellate ruling by the Third District, the case would be ripe for a writ of cert to the Supremes, although I doubt that court wishes to hear argument at this time.
As far as separation of church and state, that's a somewhat muddled area and it is the argument of the proponents of "intelligent design/creationism" that their position is not one of "religion" but of an alternate "scientific" theory that addresses holes, omissions, and problem areas left unexplained by Darwinian evolutionary theory.
The defendants in the case you describe, therefore, are claiming not to be propounding religion, but [pseudo]science, while the plantiffs are clearly arguing that the addition of creationist/i.d. to the curriculum is merely a front for forbidden evangelical Christian literalism to be introduced into the classroom, at tax payer expense, in the guise of something else. That is merely one of the issues the court will have to decide. The court will also be hearing expert testimony from a variety of scientists on the validity of the creationist theories (

) and the claims made by creationists against evolution to determine if it is, in fact "science."
When all is said and done, I expect the district court to find that the teaching of creationism is NOT required nor demonstrably scientifically based, the Third Circuit will affirm that decision, and the US Supreme Court will deny certiorari.