I just finished responding to you on the other forum

It sounds like you opened the sample MS2 Extra project and it is set to open by default.
What you need to do is create a new project for your setup. So from the File Menu:
File --> Project --> New Project
or press CTRL + N
Then a wizard will come up to create a new project for your controller. Either Select the right ini or click detect.
If you download the latest beta (0.999.6) it has help files for setting up a new project.