I've been asking around a few threads here and at XDA how to get into the boot partition of my SD card without an external card reader. I had installed CM7.0.2 to my SD card, leaving the stock OS 1.2 untouched on the internal storage (eMMC), using verygreen's method:
http://forum.xda-developers.com/show....php?t=1000957
and anamardoll's instructions (I skipped down to "what you'll need" and only watched the 2nd and part of the 3rd video, using verygreen's steps from there):
http://www.anamardoll.com/2011/04/er...e-on-nook.html
IF YOU HAVE A MicroSD READER OTHER THAN THE NC, YOU CAN STOP HERE (unless you're curious

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I was able to flash the bootable image to my SD card over USB to the Nook, once my PC recognized both the NC and SD card as removable drives. I was also able to drop the CM7.0.2 ROM into the boot partition at that time. I disconnected USB and rebooted, installing CM7.0.2, but from that point forward I had no access to the boot partition, which meant I could not install the google apps package, which meant no market
What got me into the boot partition and rendered my configuration much more flexible in general was simply going into the ROM Manager app on CM7.0.2 and choosing the first option, "Flash ClockworkMod Recovery." THIS OPTION WILL INSTALL CWM TO YOUR INTERNAL STORAGE. It will not, however, as far as I can tell, alter your stock OS in any way. I was still able to read epub, pdf, and the sample kids' book, and install a free app from the B&N market.
This arrangement gives me four boot options:
1) power on with SD card inserted, and I get CM7.0.2, which is delicious.
2) hold home (n) key and power on with SD card inserted, and ROM Manager will check for new ROMs and the gapps installer.
3) power on with SD card ejected (not necessarily removed) and I get stock 1.2.
4) hold home (n) key and power on with SD card ejected, and I get CWM, which gets me numerous back-up, restore, mounting and install options.
By inserting the SD card after CWM loaded and plugging the USB cable into my PC, I was able to navigate down to "mounts and storage" using the NC volume buttons, select it using the home (n) key, then choose "mount USB storage," which gives me access to the boot partition (and only the boot partition) of the SD card in Windows. Drop in the gapps zip file (or a new ROM if you like), "Safely Remove Hardware" in Windows, unmount in CMW, power off, then power on using option #2 above, and voila, market installed
A couple things to consider: CWM will replace the NC's stock recovery utility, meaning the "hold these buttons for so long, so many times" method of restoring factory settings will no longer be available. Also, to state the obvious, flashing CWM to internal memory will void your warranty if discovered. I found this method and the resulting configuration pretty ideal, as I wasn't much worried about my warranty and am confident in being able to "undo" by other methods if necessary. I don't anticipate much trouble updating the stock OS--if anything, the next update might wipe out CWM, or simply not take, in which case I'll wait for a CWM compatible ROM. I was originally planning to dual boot from internal storage, but CM7.0.2 is running so much faster than the stock OS as it is, and this set-up is so convenient, I'm leaving it as-is until want to pick up a higher-capacity SD.
The SD model does matter! I went with an un-classed (so, probably 2) 16GB Sandisk, recommended along with some others in this thread:
http://forum.xda-developers.com/show....php?t=1005633
I hope this has been helpful, or at least informative, to someone
ETA: Thanks to jasoraso for tracking down this thread with tools to restore the NC's stock recovery if you no longer want CWM on the eMMC:
http://forum.xda-developers.com/showthread.php?t=914690
ETAA: A perhaps simpler solution to my original problem, accessing the boot partition of my CM7 SD:
If you insert the CM7 SD after the NC has started booting from eMMC, but before the stock OS loads (for instance on the blinding white "Nook Color" splash screen), the NC will load up the SD boot partition as storage. You can then connect the NC to your PC over USB, and the PC should read both the NC and the boot partition of the SD as storage. From there, you can drop in any update package you like, disconnect, and boot by method #2 above.