I have one file that I want to add to my XP install, but I don't know where to place it or if it will work. The file is a .dll so it would need to be placed in the System32 folder. Do I just click the "add additional files" or whatever button and then drag and drop it?

I pretty sure this next thing isn't possible at all, but it's worth a try. All my programs are portable so I don't have to install them. I back them up on another partition on my HDD and would like to know if there's any way of having nLite copy them from their directory to the Program Files folder.

Just copy the file in the folder structured in the root of the Windows ISO you're making:

$OEM$\$$\system32\

http://unattended.msfn.org/unattended.xp/view/web/18/

Then click make iso and it's inside and will be copied automatically, this is Windows feature if OEM Preinstall is enabled in the unattended page.