"So if we are going to take I am guessing the ICE to Wurzburg we would go to the Fernbahnhof..."
The type of train and the station you use is a choice, not a guess. The fastest connections (which will require full-price tickets) use IC or ICE trains and will depart from the Fernbahnhof. The regional trains (take about 1 hour longer; use cheap daypass options like the Quer durchs Land ticket) mean you'll be heading to the Regionalbahnhof. I reviewed these ticket/train options here:
Some departure times require a change at Frankfurt's main station or elsewhere, while some put you on a direct train to Würzburg. The DB itinerary page will answer your questions about types of train and where you change trains, platform numbers, etc. for the specific departure times from FRA that you are considering; remember to click on "only local transport" if you want the cheaper, slower regional train options:
If you have questions once you're at the airport station of your choice, you will no doubt find an English-speaking DB employee at the ticketing office who can help.
Best wishes for a pleasant trip.
Edited: 7:08 am, December 18, 2012