Understanding usage with panels( how to use in Panelizer)

hi
My is somehow related to Understanding usage with panels and views (2187387) but need more specification about how to use this with panelizer.

Panelizer is know to let override , native display settings provided by drupal so anything/changes , for any display takes effect when done for Panelizer settings..

So how will this module work ? ( Should we just set it up as recommended in native display and panelizer will consider it , or a specific feature request should be made to make it settings been listed together with cache option existing in "Panes" settings ?

thanks