To replace the default icons (the ones with the .icns extension), all you have to do is hold the [ctrl] key and click on Safari. This will bring up a menu. The menu item we're interested in is "Show Package Contents". Select it.

Now open the Contents folder and inside of it is a folder named Resources. That's where all the graphic goodies go in OS X applications and that's where you'll drag these icons. Then relaunch the Finder to see the result. If you keep Safari in your Dock, you'll have to quit Safari, remove it's icon, then place Safari with the new icon in the Dock.

That's it!

"What are the other files?"

Those are the matching graphics that are used by the Help Viewer. They go here:

Safari.app/Contents/Resources/English.lproj/SafariHelp/gfx/

I highly suggest making backups of the originals so you'll still have them if you change your mind later. Simply adding "back" to their names is all you need to do.