I think Helo definitely first fell in love with Boomer, but after four years of living with Athena is in love with Athena now. But until now, he's never been confronted with the fact a part of the person he loves was someone else - after all, the Eight he met on the basestar who had accessed Athena's memories still was distinctly another person, neither Boomer nor Athena.

Re: Kara - one thing I'm very curious about, if she is capable of being reborn and that explains the existence of her dead body, where did the second body and the new identical ship come from? Who grew/manufactured it? Clearly, it can't have been either one of the Seven nor of the Five. Which would mean either that the original 13th Tribe, who had resurrection technology, weren't completely wiped out (with the exception of the Five)... or maybe that Daniel is still around and somehow responsible. We'll see.

I think I figured out why Cavil would want Hera, btw. After all, he was trying to make Ellen build new resurrection ships for him, which she said she needed the other four for. Now they wouldn't do it voluntarily if Cavil asked, but they might do it if blackmailed with Hera - that she otherwise would die - as they see Hera as the future.