Using/Modifying Template

[youngtly]

Just got your layers book and am looking forward to jumping in. I have a CRE Loaded template for a new ecommerce website and have to update it to reflect my logo and website header which I still have to create. I have CS4 Web Premium. I have opened the graphic source file which contains hundreds of layers. Do you have any suggestions on how to approach this task in figuring out how to find the layers I need to modify and any organization tips on how to not destroy the template? I have also been trying to determine which program to use -- Photoshop, Illustrator, or Fireworks -- to create the logo and header.
Thanks,
Terry
Las Vegas, Nevada