Hi Niklas.
When I got these type of questions, I look at how MFGtool does the flashing. Inspecting this file, the fist task is booting a temporal u-boot and kernel, using a ram filesystem (initramfs). Then it 'dd' u-boot and kernel to /dev/mmcblk0 (/dev/mmcblk1 is for the SD card), then in creates a partition on that device, /dev/mmcblk0p1, and untar the real filesystem there. here are the details:
<LIST name="SabreSD-eMMC" desc="Choose eMMC Linux 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="$ dd if=/dev/zero of=/dev/mmcblk0 bs=512 seek=1536 count=16">clean up u-boot parameter</CMD>
<CMD state="Updater" type="push" body="$ echo 1 > /sys/devices/platform/sdhci-esdhc-imx.3/mmc_host/mmc0/mmc0:0001/boot_config">access boot partition 1</CMD>
<CMD state="Updater" type="push" body="send" file="files/u-boot-mx6q-sabresd.bin">Sending U-Boot</CMD>
<CMD state="Updater" type="push" body="$ dd if=$FILE of=/dev/mmcblk0 bs=512 seek=2 skip=2">write U-Boot to sd card</CMD>
<CMD state="Updater" type="push" body="$ echo 8 > /sys/devices/platform/sdhci-esdhc-imx.3/mmc_host/mmc0/mmc0:0001/boot_config">access user partition and enable boot partion 1 to boot</CMD>
<CMD state="Updater" type="push" body="send" file="files/uImage">Sending kernel uImage</CMD>
<CMD state="Updater" type="push" body="$ dd if=$FILE of=/dev/mmcblk0 bs=1M seek=1 conv=fsync">write kernel image to sd card</CMD>
<CMD state="Updater" type="push" body="send" file="mksdcard.sh.tar">Sending partition shell</CMD>
<CMD state="Updater" type="push" body="$ tar xf $FILE "> Partitioning...</CMD>
<CMD state="Updater" type="push" body="$ sh mksdcard.sh /dev/mmcblk0"> Partitioning...</CMD>
<CMD state="Updater" type="push" body="$ mkfs.ext3 -j /dev/mmcblk0p1">Formatting rootfs partition</CMD>
<CMD state="Updater" type="push" body="$ mkdir -p /mnt/mmcblk0p1"/>
<CMD state="Updater" type="push" body="$ mount -t ext3 /dev/mmcblk0p1 /mnt/mmcblk0p1"/>
<CMD state="Updater" type="push" body="pipe tar -jxv -C /mnt/mmcblk0p1" file="files/rootfs.tar.bz2">Sending and writting rootfs</CMD>
<CMD state="Updater" type="push" body="frf">Finishing rootfs write</CMD>
<CMD state="Updater" type="push" body="$ umount /mnt/mmcblk0p1">Unmounting rootfs partition</CMD>
<CMD state="Updater" type="push" body="$ echo Update Complete!">Done</CMD>
</LIST>