Here are the steps for the Debug configuration. Same idea for Run configuration.

• Debug it once. This will create a default configuration for it.
• Right-click on file in Project Explorer or Navigator
• Click Debug As
• Click Debug Configurations
• Click Perl Local
• Select the file (should already be done)
• Click Arguments
• Type in the arguments in Program arguments

To set @INC to find your project's modules:

• Right-click on the project in Project Explorer or Navigator
• Click on Properties
• Click on Perl Include Path
• Click on "..."
• Locate the base path of your modules
• Click Add to List (will look something like ${resource_loc:/project/lib})