I usually don't bother trying to reload transports. I usually put them on a planet when they get depleted and decommission them.
Any legions left, re-enter the pool and I build new, usually better transports.
Note: Its usually faster to move legions by decommissioning transports from old wars on the other side of the galaxy from the current war, then to move them across your space. I build new transports on the current front line with the re-pooled legions.