Hi Rich,
the best way would be to export your clips from premiere as a self-contained file.
afterwards import them into encore if you need specific chapter-marker and let encore encode the clips with the chaptermarker on the timelines.
if you wont need specific chaptermarker on a specific TC you an also do a bach-prozess within adobe media encoder to create your assets.
if you starting encore make sure your project-settings are 720p59.94 if not, all your material will be scaled to the selected format (1080 for example).
als be awared that you can´t use different input-materials with encore as the BD-spec normally allow.
all stuff will be scaled/transcoded to the selected setting.
and finally – yes, 720p59.94 is part of the BD-specs.
cheers
danny