Shafts, as well as complete cues should be kept in the same environment as you keep yourself. In your home with reasonable temperature and humidity considerations. Temperature extremes should be avoided.
Shafts, and butts should, in my opinion, be kept laying flat. If a shaft is kept in an upright position a preponderance of weight bears on one end and over time can cause a warp, whereas a shaft when lying flat has it's weight more evenly distributed. Same goes for the butt. Hope that helps.
Keeping them inside the case is fine. If outside the case, make sure they are protected from damage. :smile: