Ok so just going to give you a quick run down on the 4 types of storage in android devices prior to Honeycomb.
Up until android 2.3.x storage was really broken into 4 areas: 1.Rom (Boot Partition, Core Phone software), 2. System Storage (Data files, and some of the stuff that can be manipulated via root access), 3. USB Storage (internal SD Card that is left over after 1 and 2 are made. Sometimes doesn't exist), 4. SD Card (The micro SD Card, pretty self explanitory). The storage that comes with a device internally is split between the first 3 types. That is why on samsung phones with 16GB internall storage you only end up with between 10-13GB depending on the phone. The 10-13GB are what is left after the first 2 partition areas are created. Because the Note has allot of special stuff for the digitizer and S-Pen we are in the lower end of that spectrum.
When you load a app it goes in the System storage. Samsung is nice in that they allow 2GB for System storage. Allot of manufactures didn't provide such a nice amount of space to load apps. My guess is that you are coming close to filling up that storage. Depending on weither you upgraded to ICS or not, the process will be slightly different. What you need to do is go in to settings and then applications and look for the options to move them to the USB Storage(it may say SD Card). Not all apps can move to SD Card and some apps you absolutely want to depending on size. It should also be noted that this won't move the entire app, just certain parts. Becuase of that it is still possible to run out of system storage.
This changed in Honeycomb and above with all internal storage being completely usable by the system no matter what. There are some technical reasons for why they can't fix this on older devics upgraded to ICS and above, mostly has to do with fear of bricking the device.
I hope that answered your questions. I am in the same boat you are as if i didn't move about 3GB of app data to the sd card my system storage would of filled a while ago.