How To Install Windows Server 2003 or Windows XP Media Center Edition 2 CD from a bootable USB
Some Windows 2003 Server and Windows XP Media Center Edition installations needs second CD to be installed, but WinToFlash doesn't provide second CD selection. The installation package looks like this:
Merge installation CDs
If asked for "autorun.inf file already exists, replace or skip" select skip.
Select resulting folder in WinToFlash
Don't check the "Use my ISO...", WinToFlash will use your folder as a source.
On the page "Process steps" select "Transfer all folders from original image"