If you want to capture a custom order field in Brightpearl for shipping instructions, eg. 'Leave behind the gate'

You can do this from the Brightpearl settings within Shiptheory. At the bottom of this page on the left, you'll see a small cog icon, click this to reveal some of the advanced settings. Under the advanced settings you'll find the option to specify 'Instructions Custom Field' Here you should put the field code of the Brightpearl custom field. These traditionally start PCF_SOMETHING. Eg. PCF_INSTRUCTIONS 

Make sure you hit save when you're done. Now any new shipments that are pulled down by Shiptheory for orders in Brightpearl that have instructions will get sent to the carrier (for carriers that support instructions/notes).