When you export a method, you always provide a template file. The template file contains all of the settings which Skyline does not know anything about, and then Skyline fills in the other parts of that with the peptide-specific information from your document.
I believe there is no way to tell Skyline about the thresholds which trigger the mass spectrometer to start collecting MS2 spectra, so I am thinking that those already need to be specified in your template file.
Please let us know if anything goes wrong when you try to export a SureQuant acquisition method. You can send us your Skyline document and .sky.zip file and we can make sure it gets fixed or ask our contacts at Thermo how this is supposed to work.