OneNote uses the capabilities of the Windows XP Tablet PC Edition operating system for its ink support. So on a Tablet PC, you can capture ink in OneNote with the Tablet pen, or a mouse, or a third party digitizer pad or pen. However, the quality of the ink that is captured will vary with the device and with the software driver that it uses. For example, the tablet pen can capture your ink at over 130 samples per second. This means that a lot of data is captured about the motion of the pen, and as a result, the quality of the ink that results will be better. Likewise, the quality of handwriting recognition will be better. A mouse or external device that uses the mouse interface will sample at around 40 samples per second resulting in lower quality ink and handwriting recognition accuracy.
When you are not on a Tablet PC, OneNote no longer has access to the handwriting recognition engines of the Tablet PC. As a result, although you can still capture digital ink in the same ways as on the Tablet PC, the sample rate will be the lower 40 samples per second, and the ink cannot be converted to text. The ability to search handwriting is also dependent on the recognition engines. Therefore, that capability will not be available either.
As a result, when you are not on a Tablet PC, OneNote treats all the ink that it receives as a picture or drawing, and not as digital ink. With a picture or drawing, there is no ink searching and no ink recognition capability. The commands to treat ink as handwriting are also unavailable when you are not using a Tablet PC.
Some add-on pen peripherals have additional capabilities of their own to capture images of your handwriting. Such pens may be able to integrate with OneNote in a limited way, such as by pasting a bitmap picture of your writing (as opposed to true digital ink), but this will depend on the manufacturer's software.