You can, but you need to disable the KoboTouch driver when you want to treat it as an external drive. Then when you have the device connected, you can either use save to disk or connect to the device as a folder device. Doing the latter means you can select a folder on the device to store the books in and calibre will scan for books and use the device list to show the books on the device.
If all you intend to do put the books for use with KOReader in different directory, you can use save to disk to copy them there when the KoboTouch driver is enabled. If you do this, name the directory with a "." so that nickel doesn't attempt to process them.
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