Ability points (denoted by a + sign on the ship in the Empire Tree) are points that can be used to acquire/upgrade abilities for your capital ship.
Command points (denoted by > in the Empire Tree) are points used for strike craft squadrons (one point = one fighter OR one bomber squadron).
Capital ships get one ability point every time they level, and once assigned, cannot be resassigned to another ability. Level 2 upgrades for regular abilities are unlocked at level 3, the level 3 ability upgrades are unlocked at level 5. Ultimate abilities are unlocked at level 6.
Command points become available depending on both the capital ship type and level (example, carriers will eventually have 6 squadrons, whereas planet bombing ships will only ever get 1 squadron).
