As long as Custom Labels are equal to your SKUs in Linnworks, the system can use them to link your Linnworks inventory items to your listings automatically.
To add a custom label, open the screen that lets you view your listings on eBay, and in that table there is a 'Custom Label' column. If you do not have a custom label, the value in that cell will be [Add], and you can click it to add a new custom label. Remember to click Save after you have added the label.
For more information on adding the Custom Label column on eBay, please refer to this short video guide.