Use whichever mode seems to be the most robust and compact. As Ode mentioned, for car-bots this is usually car mode. For trickier modes, I make little cardboard open ended boxes (3 or 4 sided). Cut the cardboard to appropriate size then fold around the figure. EG, long open ended triangular box works well for helos to protect the blades. I've used this technique to transport figs in check-in luggage (using both suitcase and soft-luggage). Can wrap fig in bubble wrap beforehand for extra protection, and tape accessories to the inside as well.
Given the length of storage time, and depending upon your 'storage containers,' I would also suggest using ziplock bags as well to keep moisture, insects, etc, out.