AT in Tagalog can be used in different ways but it is mostly used as "and" or "that". when you will use NA the sentence would goes like this... "Masaya kaming lahat NA makita kang muli."

I really cannot explain that logically. But it sounds right , archaic, native, authentic,clear, friendly and beautiful to use AT. Maybe we can put it this way, We are so happy that at last, that finally, at long last...we have seen you again. At here doesn't mean "and", but a way of saying at last, or finally... There's this implication of excitement, of having had to wait so long and being so happy to have finally seen what has long been being anticipated about.

salamat sa pagsagot ^_^

In daily conversation, it would go something like this, "Masaya kaming lahat na nakita ka namin ulit."

BTW, "Salamat ng maaga" comes across as "an early morning thank you". I think "Maagang pasasalamat" would sound better. "Inuuna ko na ang pasasalamat" would most likely be how we'd say it.