you should experiment. One of the primary goals in creating VC was to make it possible for people to customize it to suit their own needs. You just need to make a copy of your folder as a backup before you go crazy changing stuff. For beginners you should start by only modifying the items in the tree known as "phrases", until you gain a better understanding of the program.
The check box near the green microphone is for what I call "intercom mode". With eventghost you can get VC to listen to just one command (the box will be checked) and then it will automatically turn itself off after executing one command.
There is currently no automatic way to run GenXML but I will probably add some kind of feature to address that. I still need to do a bit of work on GenXML first. Also, VC will always need to be restarted after performing a GenXML.