Please provide screenshots or log files of the failure you are seeing.
Skyline Batch supports a somewhat limited set of workflows. Your most flexible option is still to write your own command line batch file to run SkylineRunner or SkylineCmd.
Have you looked through the tutorials and companion webinars to understand what it can do? For instance, it currently expects you to provide a template Skyline document with all your settings into which you will import raw data files. It does not support any method to import targets (e.g. transition lists) into a targetless document with only settings as you seem to be hoping for.
Hope we can help you mor to make use of this powerful new tool. Though, for now, you likely have to adapt your expectations to what it can actually do, and then request what more you might hope for.
Of course, it should not crash on initialization.
—Brendan