If your template consists of PNG files the entire size of the page (e.g. 2400x2400 pixels) then you should really crop them before adding them to SBM as embellishments.
You can perform the cropping in SBM, however in the current version (126.96.36.199) doing so will dramatically reduce the quality of those embellishments when optimized during exporting, because of the dramatic difference in size between the cropped object and the original image file (which is mostly blank transparent space).
In the next update to SBM, the "Optimize embellishments" feature will permanently apply any cropping that has been done to embellishments, so you will be able to perform the cropping within SBM with no problems when you export to a template. However I'd still recommend cropping the image files externally.