I'd see Lisbon in two days and reserve the third for a daytrip to Sintra which is an especially wonderful destination for couples.
As for suggested attractions, it really depends on your interests, If you like museums, streetlife, etc. This Lisbon Itinerary may be helpful.
Weather in late September may be either still warm and sunny or the beginning of the rainier season. But it's one of the best times to visit because the August tourist crowds are gone (although Lisbon is way less touristy than other European capitals).
Although the city is very hilly, you can walk to just about anywhere in the old center (except to the district of Belem which has some of the main monuments and museus, for which you need to take the tram).
As for accommodation, I'd recommend the following neighborhoods: Chiado, Baixa, or Bairro Alto.
They're all close to each other, with restaurants, cafes and bars just around the corner from any hotel or apartment.
Finally, Lisbon is a very old and romantic city, and couples enjoy the sunrises and sunsets: The Best Sunrises and Sunsets in Lisbon