Even though Freescale hasn't implemented the WinCE7 MFGTool for iMX6, I think the Linux MFGTool can also be used for WinCE Image burning.
For example, you can edit the ucl2.xml in MFGTool, added the followed item to burn eboot.nb0 to eMMC address 0x400 and burn the nk.nb0 to eMMC address 0x80400.
<LIST name="WinCE7-SabreSD-eMMC" desc="Choose eMMC as media">
<CMD state="BootStrap" type="boot" body="BootStrap" file ="u-boot-mx6q-sabresd.bin" >Loading U-boot</CMD>
<CMD state="BootStrap" type="load" file="uImage" address="0x10800000"
loadSection="OTH" setSection="OTH" HasFlashHeader="FALSE" >Loading Kernel.</CMD>
<CMD state="BootStrap" type="load" file="initramfs.cpio.gz.uboot" address="0x10C00000"
loadSection="OTH" setSection="OTH" HasFlashHeader="FALSE" >Loading Initramfs.</CMD>
<CMD state="BootStrap" type="jump" > Jumping to OS image. </CMD>
<CMD state="Updater" type="push" body="$ ls /dev/*"/>
<CMD state="Updater" type="push" body="send" file="files/eboot.nb0">Sending EBOOT image</CMD>
<CMD state="Updater" type="push" body="$ dd if=$FILE of=/dev/mmcblk0 bs=1024 seek=1 conv=fsync">write eboot image to sd card</CMD>
<CMD state="Updater" type="push" body="send" file="files/nk.nb0">Sending NK image</CMD>
<CMD state="Updater" type="push" body="$ dd if=$FILE of=/dev/mmcblk0 bs=525312 seek=1 conv=fsync">write nk image to sd card</CMD>
<CMD state="Updater" type="push" body="$ echo Update Complete!">Done</CMD>
</LIST>