When using Hades, you only have control direct control over the undead figures you summoned that turn. Each and every movement using Hades must contain an undead figure. However, regular figures are allowed to join in with each movement, as if being lead by an undead general.
Undead troops can move over normal ships. Normal ships must have an undead ship if the ships want to move, however.
And does it work the other way around? Can you move an army of just normal troops over undead ships with Hades?
Movement with Hades must always include at least 1 undead troop when moving an army, or 1 undead fleet when moving ship(s). The type of ships have nothing to do with Troop movement. The only way you could ever move an army of troops with Hades is if there is at least 1 undead troop included in that army.