When a druid prepares his spells he spends 1 minute per spell level, and to change the list he needs a long rest.
If the druid can prepare at least 6 spells, but he only prepares 4 of them after a long rest, can he prepare two other spells at some other time? Or does he need to prepare them all at once.
(PHB, p. 66) When you prepare your spells, you the number of spells you choose is exactly equal to your druid level + wisdom modifier. There is no option of choosing less spells than that given in the text. Therefore, there are never any free "slots" in your spell list to fill later.
(PHB p. 66, emphasis mine) Directly after a long rest, you can can prepare a new list, but as per the rules above, you have to choose all of the spells at once.