Use BCDedit when Windows is not the primary disk

Congratulations, you've decided to use some other boot loader to as your primary and simply chainload bootmgr for Windows.  Unfortunately you still want to modify the configuration of bootmgr, but BCDedit doesn't do work unless you admit it's god of your boot process.

BCDedit by default opens the configuration for the very first disk in the system.  If that doesn't happen to be Windows, or the Windows installation you want, then it just won't open it.  To get around this you need to mount the system reserved partition which windows creates for the BCD configuration to live on, and then specify that you want to modify that store in your configurations.

First, under disk management, find the 100MB system reserved partition and give it a drive letter.

The BCD configuration will be at (drive letter):\boot\bcd.  To specify this in BCDedit use the following syntax:

bcdedit /store (drive letter):\boot\bcd (your command)

Credit: Information for this was gathered from numerous websites in addition to independent research.  This project came up as a component of my plan to run ESXi 5, Windows 2008 R2, RHEL 6 and XenServer 6 all on one box.  Booting ESXi and Xen (both which use syslinux) did NOT work, despite being referenced in the image above.  Further details can be found in the blog post on that topic.