For most of the deck markings, no, it's not going to matter, although it does depend on what time period you're building your Big E to represent. For the best current info on deck markings and layout, updated armaments, etc., you need to go to the Navy News website, http://www.news.navy.mil/, and check out Enterprise photos. There are quite a few from her last two deployments.
The only things lacking from the Starfighter sheet for a current Enterprise are the bow flight deck numbers, they are now hollow white lines, and the ship's name for the forward and aft island locations.