Where are apps natively stored on a Nook running CM7 off a micro SD
I would just repartition the SD card so that the first partition is larger.  AFAIK the system doesn't rely only the partition size, just the order.

You could, however, run su then pm setInstallLocation 2 in a terminal on the device, or from adb shell, assuming you have root.  That will make installs default to the "SD card", your second partition.