After creating your Connection and before you create a Report Task you need to create a Report to add to that task. Take a look at the relevant links here: How to Create Tasks
If you wish, you can create more than one Connection, each to different QlikView documents. During the Report creation process you will have an opportunity to select the Connection you want to use objects from.
Once objects are added to the report the Connections field is populated. For example this Report uses objects from 2 connections:
You use Server to automate the scheduled Jobs created in Designer. How to Configure QlikView NPrinting 16 Service
I suggest you go through the tutorials to familiarize yourself with the many powerful features of Qlik NPrinting. QlikView NPrinting 16 Tutorials - Setup
HTH - Daniel.