Simultaneous Games

[Suicide Junkie]

If you want the ships to move together, either fleet them, or shift-click them to give them a combined order.

The shift-click-order method makes a virtual fleet out of any number of ships and/or fleets, and they will move together.

Not sure about the colony ship... did you watch the replay, or just see a colony ship at point A on turn N, and a new colony at point B on turn N+1?
It could be two different colony ships you're seeing.
In order to move 9mp in the unmodded game, you'd need engine up grades or solar sails, and propulsion experts could help.
Modded, anything goes.

If both of your fleets were moving towards each other, and had the same speed, they could have each moved on the same day, swapping places. You'd then be behind them.
Its best to force the enemy to come to you if possible.

If you were cloaked, your ships may have chased them, but not attacked, staying hidden instead. Stealth armor maybe?