Windows ISOs on the 2nd partition (E2B v1.A7+)

If you have a large (>128GiB) USB hard disk, I recommend that you use the first partition (up to 128GiB in size) for E2B and use the second partition for other purposes such as for storing utilities, hard disk backups, documents, etc. Note that only  recent versions of Windows 10 (1703+) can access the 2nd partition if it is on a Removable (flash) drive.

However, you can place most payloads such as linux .ISO files, Windows VHD files, etc. on the second partition and add the PTN2_MNU.mnu menu file (find it in the \_ISO\docs\Sample mnu Files folder) to one of the standard E2B menu folders (e.g. add it to \_ISO\MAINMENU). The PTN2_MNU.mnu will take you to a sub-menu where all the files in a folder on the second partition will be listed and you can then boot to any one of them.

Note: Windows VHD files will only boot from partition 2 on a Removable USB drive if the VHD contains Windows 10 1703 or later. However, there should be no restriction if the USB is a hard disk.
Starting with E2B v1.A7g Beta, it is possible to also run Windows Install ISOs from a second partition on the E2B USB drive.
This assumes that your E2B files are in the first partition and you have created a second Primary NTFS or FAT32 partition on the E2B drive (and have removed the very small 2nd partition that Make_E2B.exe usually makes). 
Check that only two Primary partitions are present using 'RMPrepUSB.exe - Drive Info - 0'.
Note that some BIOSes have a bug in their USB driver and they cannot access files past 128GiB, so if the 2nd partition is beyond 128GiB you may experience strange grub4dos errors, etc.  E2B will warn you if the BIOS is buggy when it first boots. Sometimes you can fix the BIOS driver by loading the grub4dos USB 2.0 driver (use a USB 2 port instead of a USB 3 port).
If booting Windows ISOs from an E2B 'fixed-disk' USB drive, you must also connect a WinHelper 'Removable' USB flash drive so that Windows will load the XML file and use ImDisk to load the ISO file as a virtual DVD drive.

Choose a Windows ISO from ptn2

This example is for a Windows 10 ISO (XP ISOs are not supported on partition 2).
  1. Copy the whole \_ISO\WINDOWS\WIN10 folder to the second partition so that there is a \_ISO\WINDOWS\WIN10 folder containing the standard XML and .key files, etc.  Do NOT copy the \_ISO\WINDOWS\installs folder - this must only exist on partition 1.
  2. Copy your Windows 10 ISO to this new folder.
  3. Create a small dummy file (of identical name and path of the ISO) in the first E2B partition. An easy way to do this is to copy and then rename one of the .key files. Any small file can be used but it must be greater than 0 bytes in size. e.g.
Partition 1
\_ISO\WINDOWS\WIN10\Win10x64.iso (any non-zero size - any contents)
Partition 2
\_ISO\WINDOWS\WIN10\Win10x64.iso  (5GB) + folder contents
Now you can select the ISO from the Windows menu as usual (all .iso files will be listed), but E2B will detect if there is an identical ISO on the 2nd partition and will use that instead. E2B will also prompt you with a list of the .xml and .key files that are present in the second partition if the selected ISO is in the second partition.
You can add any number of ISOs in the same way.
If you want to delete the ISO, remember to also delete the small dummy ISO file on partition 1 or else it will still be listed in the Windows Install menu (but it will display an error if you try to boot from it)!
Note: If your E2B USB drive is of the Removable type (flash drive) then this method will only work with later versions of Windows 10 (1703 and later), because earlier versions of Windows can only access the first partition on a Removable drive.

Add a menu entry for an ISO on Partition 2

You can add a .mnu file into a menu folder (e.g. \_ISO\MAINMENU) to directly boot to one of the ISOs in partition 2.
A 'dummy' small ISO file on partition 1 is not required. 
You can also specify an XML file if you wish.
See the sample menu file "\_ISO\docs\Sample mnu files\Windows\Win10_8_7_ISO_on_PTN2.mnu" for an example.
Copy the .mnu file to \_ISO\MAINMENU folder and then edit the file to change the ISO name, etc.
If you want to be prompted to choose a key or XML file, use set XML= in the .mnu file.

Install Windows from a 'True Hidden' E2B drive

If you use the 'True Hide' option (as added by the PimpMyDrive.cmd script), then it is possible to completely hide and make inaccessible the first NTFS E2B partition from Windows OS's. You can still MBR-boot from it to the E2B menu and run most of the payloads (with some exceptions such as some WinPE WinBuilder ISOs and other Windows-based payloads).
However, it means that you cannot install Windows from the hidden partition because Windows cannot find the ISO file. 
Here is a rather complicated way around it!
Note: If using a Removable E2B USB drive, this only works for Windows 10 1703 or later. 
For E2B 'Fixed-disk' USB drives, you must also connect a WinHelper Removable USB flash drive.
1. Ensure the E2B partition is accessible - unhide the E2B drive by booting to the E2B menu and choosing the True Unhide (hd0,0) option.
2. Copy the \AutoUnattend.xml and \Unattend.xml files to the root of the 2nd partition
3. Copy the whole \_ISO\e2b\firadisk folder to the 2nd partition (keep the same folder structure)
4. Copy the Windows ISOs to the 2nd partition (as described above) and make a small dummy ISO in the first partition of the same name (see 'choose an ISO from ptn2' above for details).
5. Boot to the E2B drive and run 'True Hide (hd0,0)' to hide partition 1.
You should now be able to boot to the E2B Windows menu, pick an ISO and then install from it. You can also use a .mnu file (see above).
Partition 1:
\_ISO\WINDOWS\WIN10\Win10x64.iso (any non-zero size - any contents)
Partition 2:
\_ISO\e2b\firadisk folder
\_ISO\WINDOWS\WIN10 folder + \_ISO\WINDOWS\WIN10\Win10x64.iso  (5GB)
Note: SDI_CHOCO is not supported if the E2B partition is hidden, because Windows will not be able to find the SDI_CHOCO configuration files later on!