It matters not the way in which you place the cue inside it's case. More important is the care with which you handle your cue when in use and when inserting and removing it from the case.
Here is an image of someone inserting but and tip down:
Here is an image of someone inserting the two joint ends down, with butt and tip pointing up:
But, here is what I do. For ease of deployment, I insert the butt end down, with that joint at the top. Then I insert the cue tip portion facing up.
The reason I do it this way is because when you pull the cue tip straight up, the bottom joint of that part is immediately inline with the joint of the other part. you can screw it in at this point, and then haul the whole cue out.
Plus, it just looks smoother that way.