If you want to use external partitioning you have to export the whole device via USB.
When you are running Harmattan and connect USB in memory card mode, you are just exporting one partition (by default /dev/mmcblk0p1 which is your MyDocs)
There is no way you can partition the device as the parts that contain partition infomation are not exported.

When you boot into MOSLO or ubiboot maintanance kernel, your whole /dev/mmcblk0 is exported, also the partition tables. Hence, you can modify everything on the drive.

The thing is, you do not have to flash anything permanently if you do not want to, it is enough to jumpstart the device with a maintanance kernel (sudo flasher -k <repairkernel> -l -b)

Note that now, after you do this, your device will be in Open Mode regardless of what mode it was on before.
If you were in Closed Mode you will encounter some weirdness caused by the device aegis keys no longer matching the device mode; for example you will not be able to store passwords before you regenerate the password storage with new keys.
Also you will need to patch your loader or you will experience application shutdown when installing new applications, for example.

If you are in Closed Mode, I will always recommend that you do not enter Open Mode accidentally, but rather back up your device and enter Open Mode via the back-to-back flashing method.
When you do that, it will save you tons of grief later...

I want to repartition my N9.
I have tried the following but it did not work.
1. I exported the whole mmc over usb and made another partition from the MyDocs one.
2. Edited /etc/fstab to mount it, restarted the phone. (Didn't work, it did not mount. Anyways how do i check the mounted partitions, lsblk is not available)
3. I tried the mount command, but that too didn't work, even though i was root.

I am on stock kernel, is that why? Is open mode required for doing this??

Also i want my partitions to be more organized. Like
1. rootfs
2. home
3. MyDocs
4. Extended (Other partitions here)

How do i do that? Because flashing will just rearrange them to the way it was originally, so how to change my partition table to this after a clean flash?

1. How did you do what?
2. fstab provides easy mounting points, does not mount automatically
erm: what about mount and/or sfdisk?
3. Correct. For mount to work you need open mode.

Good luck with reorganization! that would require lots of knowledge and tinkering. On n900 it can be done with lots of efforts.

1. I used the n950 kernel and rescue initrd to export all partitions over usb and use gparted to make partition changes. (made a new partition)
2. then how come home and MyDocs get mounted at startup? i am confused, MyDocs is specified with noauto option in /etc/fstab, still it mounts automatically. So i made a new entry here regarding the newly created partition, without the noauto option (default is auto, right?) hoping it'll get mounted automatically, but it did not.
3. Thought so, thanx.

So i did manage to reorganize the partitions, it took a lot of time, but i guess is done now.
So here's what i did:

1. Flashed device with stock everything, then immediately flashed the open mode kernel (what does flashing only the kernel actually do? is there a separate partitions for the kernel or does it go in rootfs itself?)
2. used the rescue initrd to export all the partitions and took a backup of rootfs using dd.
3. used gparted to delete all the partitions on N9 and recreate them as i wanted.
4. used dd again to restore the rootfs to appropriate partition.
5. edited /etc/fstab to appropriately mount the newly created partitions.
6. Restarted hoping everything works, only to realize the stupidity. (Obviously didn't boot)
7. Installed the ubiboot kernel (This is where, it got confusing, now where is this installed? as i have moved rootfs from its the default location)
8. Changed the ubiboot.conf and preinit_harmattan to set the new location of rootfs
9. Reboot

Harmattan did boot, home and MyDocs also got mounted, but i couldn't make out if the other partitions got mounted or not, No terminal yet, no file manager.

So was/is there and easier method of doing what i did?

EDIT: the other partition didn't mount automatically, i thought it would as other partitions do.
#mount -a does mount it. How do i make it mount at every boot? Shouldn't 'mount -a' run at every boot by default?

MyDocs is a kind of special case since it needs to be mounted/umounted when exported via USB.
There's a daemon (usbmoded) that handles mounting it.

and from where does it get the information about MyDocs to mount it.
Cuz i have edited usbmoded.ini to account for the new partition.
1. It gets unmounted after connecting usb, but doesn't get mounted on the pc
2. After removing the usb, it is mounted back in harmattan
3. It doesn't mount on boot

Well, just two things really can affect it;
1. /etc/fstab
2. /etc/usb-moded/usb-moded.ini

If you have those correct and mounting is irregular, then there might be some problem in partitioning/formatting, perhaps?

what will happen if i do a factory reset? Will the phone be partitioned to stock or will the partition changes remain?

Factory reset from the phone, not like reflashing by external computer?
I'd imagine it cannot change partitioning then, since the device has no access to the firmware images. If it did repartition the device, where would it pull the new data to the device?

Yep, would say so too.
But be prepared to possibly get in trouble either way. As it might be that the reset from phone will not follow your partitioning scheme but an internal fixed one.
Furthermore when reflashing with flasher and using vanilla (eMMC) image then for sure you will see a warning and you have to confirm with a command line parameter (do not remember now ). What happens when only flashing firmware: no idea (never tried).