Calibre > Preferences > Plugins > Kobo Device Interface (or Kobo Touch or KoboTouchExtended) > Customize Plugin
Then, in the field marked "Specify a tags type column for automatic management" enter the lookup name of your custom column preceded by a #
If you also want a shelf for series, you could use something like:
#koboshelf, series
This thread has all you need to know:
https://www.mobileread.com/forums/sho...d.php?t=193184
Hope this helps.