I absolutely loved Samoa, you're going to be very glad you chose it!
In Apia, I stayed at the Outrigger which I thought was very nice and pretty decent value for money. If you're going to go for one splash-out meal, go to Sails, in one of Robert Louis Stevenson's old houses overlooking the harbour on the main street. Fantastic lobster.
Virgin Cove is a great little eco resort on a lovely bay around the other side of the island. They have a traditional outrigger canoe that you can borrow and paddle around the bay in.
For a real Robinson Crusoe experience, try Namua Island, a tiny cluster of fales on a little island off the coast of Upolu. It's a blissful situation on a lovely lagoon with waves breaking over the reef on the horizon. The family that run it ferry you over the lagoon in their outrigger - a great way to arrive. Low-tech, but fab.
I would personally choose to spend the balance of time on Upolu, 'cause I think it's a bit prettier. It is worth going to Savai'i though, particularly to see the blowholes, the lava fields and the olumoe waterfall (lovely place for a swim).
Things not to do? Personally I didn't particularly like Manase.