I think the harem endings will only become available when you've reach a certain level of harem acceptance with specific characters. In my playthrough I've unlocked four harem endings, but there could be more(?)
- Sen and Lady Minna
- Theo, Uno and Vera [housemates harem]
- Elisa, Irene and Theo [Shinyrost harem]
- All seven women (everyone reached harem acceptance cap except Rachel with only Lv. 3, I can't raise it further because I still haven't encountered any more harem triggers with her)
The game will actually tell you when you're about to reach the good ending with a partner. Selecting otherwise will just open the character up for their harem endings. I would suggest creating a save whenever a choice is presented to you, frankly I have no idea what happens after you get married to just one woman.