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If you tell it your prime output, it creates settings based on that. You can still produce any of the other outputs from whatever you select but there will be some simple changes. Principally, the window options are different for CHM and webhelp. If you create a new window, it is based on your default layout but, as I said, you can always change that.
RH asks this when you are creating a new project. Is that what you've found? You may have a standard output type for your help projects, such as WebHelp, so in that case you would select WebHelp as your output. All this does is provide the output generation settings before you run the output the first time, and it tells RH what your primary SSL is so that you can run that at the click of a toolbar button. You can output to any other SSL anytime.
Nothing is set in stone. You can change the primary SSL settings or which SSL is the primary any time you like. If you haven't decided on an SSL when you're creating the project, I'd suggest just providing as much as you know to begin with.
I don't think there's any way to get around that wizard.
Thanks for the responses,