There are variants for when you lost your virginity to him, or if you also didn't have sex with anyone else and stayed loyal to him.
For the Virgin logan route, you can't lose any virginities until you get his 3rd heart. The only way to do that is by not staying the night with Bernard at his house. You have to leave and then you'll still get the option to talk about Caleb after that. Then after you lose virginity to Logan, you can stay the night with Bernard, but if you bottom for logan you have to top for bernard in order to get special dialogue and reward during his axe throwing scene at the fair. That's because you can't gain sexual experience in the hole Logan used lol.