There are a couple of options...
1)
In your HTML page, make the path to CSS and scripts relative...
"/scripts/myscript.js"
Where the scripts folder is the first folder after the root folder
2)
You can add the base tag to your page, which means ALL page resources will be treated as relative to the root location you specify...
<base href="http://www.mysite.com">
More info about these two options.
If you can, option 1 is perhaps a bit cleaner. You know explicitly the resources that you are affecting. Using the base tag will affect ALL relative paths on your page. Images, Links, Scripts, CSS et al. The second option works best if you developed your 404 page assuming it would be in the root folder, but it could actually be referenced from any non-existent directory. You just put your root address in the base tag and it will all behave exactly as you expect.
With either option, the images can be relative to the location of your CSS file.