Given the choice, using the LFE out is better than line level on a HT receiver because the receiver handles the x-over this way. Line level means you need to manually adjust the sub's x-over to blend with your mains, unless that is what you are looking to do.
Down firing will make a slight difference in sound, but with a good sub, down vs front/side isn't one of the primary factors I would use to decide on which sub.