Difference between .Application and .Exe

[Ken]

I'm new to deploying/publishing a vb.net app in an environment in which the app will run from a shared/server drive.

When I publish, I get a .Application and an .EXE file.
.Application - WILL NOT ACCEPT PARAMETERS
.Exe - Accepts parameters, but seems like it requires the .Manifest and other files in the same folder.

When I run the deployment Setup.exe, it creates a Start Menu shortcut to the .Application ... why not the .Exe ... and why the parameter issue?

Could someone point me to a good article that deals with this info...?

Thanks a bunch!!!