Hello, and thanks for the nice words!
You can hook up with Dan regardless of the route (although of course you can't hook up with Dan when you're exclusively dating someone else). You can also hook up with the twins (and there's an achievement for doing so repeatedly), but there are no CGs associated with that. Nate and Jake are only available as a throuple... if you don't meet the requirements, they might break up, but you can't date only one of them.
There is also one very special hookup CG not associated with either one of the four standard routes or the secret route. Plus three dream sequence CGs that aren't really hookups.
Dan is actually the third hardest route in the game (although as noted, he'll happily have sex with you). The best way to raise friendship with him is by going to Q&A meetings, hooking up with him, and IMing him. Raise your confidence early so you can IM him early so you can start hooking up early. If you do these three things, it should be pretty obvious when his route branches if you've gone to Q&A in other routes (especially Malik's). The threesome decision is important (he won't date you if you turn down the threesome), but also not the point where it branches.
Libido affects nothing except the ending once you're dating Dan (it just can't be too high at the end of the game). You can safely ignore it during the game (although if you're hooking up with Dan every week, it should always be near 0 anyway).