Thank you for contacting Linnworks Technical Support.
You can integrate the APC shipping integration in Linnworks.net but you can still use Linnworks Desktop to print labels. Please follow the following link to integrate.
Please feel free to ask any further questions.
In order to print from a desktop application, you simply need to make sure that you will assign a correct shipping service to the order.
If you cannot see the shipping service in the Desktop application I would suggest checking the shipping integration Services section from linnworks.net (shipping>integrations>shipping apping>add services)
Add provides shipping services in the section, create a correct link and everything should be in order.