I don't have EPIC installed, but from the description I'd expect to see two textfields/-areas...

Your expectations are quite right;-) One area to enter the command line arguments for your program, one area to enter the arguments for Perl. It works quite well and both on Windows and Linux. There are more advanced options and other tabs in this dialog box though.

So, I'm wondering what happens with any arguments you enter there? Seems like basic functionality...

It * is * basic functionality and it works as expected, i.e. the arguments are passed to Perl and the script respectively. It works fine in practice though frankly speaking there is no need to use this functionality. Both on Windows and Linux the command line is more flexible. The only advantage I can think of is that you don't have to switch to another Window if you work from Eclipse/EPIC. It does give some nice other features.