It's going to be your decision whether you put all of crossbrowser code in one function or you split it. My suggestion is that if you don't have more than couple of places where you worry about IE and NS, write it in the same place. Otherwise, put all IE functions in one file and all NS functions in other (if you have more than these two browsers to worry, put the rest in other files), in each of your web presentation files check for the browser and accordingly use "document.write" statement to include the appropriate file in your code. This is the cleanest solution and gives you ability to manage your code nicely.
Also, NS4.x is still around and only if you or your company doesn't wish to comply with this browser, you should not allow them to see your pages. At least give them option to view textual pages or warn of problems that the page may not load correctly.
Actually I am just creating this site for a learning experience. But I want it to be as professional as possible which means creating it for 640 by 480 and nn4.7
It is easy to program for higher resolutions and the new browsers. :)