Hello lalulofi,
The one that you should be able to modify is the editor file. If I remember correctly it looks like the text file format. Modifying this file will exclude a particular file, or application from being protected under Blink's Application Protection Engine (known as "Kevlar"). This is best used when you know a program is ligitament, that you want to run, but because the program's behavior is suspicious to Blink, it is giving you that warning. There are a few other things you can read about the "apiex.ini" file in and how to modify it. One of these posts I made (when Blink Personal Edition was first introduced to the public) is located at:
http://forums.eeye.com/forums/p/54/140.aspx#140
The system protection wizard, if I remember correctly, is used to create explicit rules for things you want to protect your system from. Hence you know the exact thing that will "trigger" or set off the rule, what it affects on your system, and how you want Blink to react to protect you from it, etc.
I hope all this makes sense, if not I am sure one of the eEye folks here will pick up on your post and assist if necessary.