The main spacecraft is moving on its way to the Jupiter system. The little pod craft come out of the bay of the main spacecraft and are at its velocity. There is no friction in space and the little pod craft are in the same frame of reference relative to the main spacecraft. Therefore, from the frame of reference of the pods, the main spacecraft is stationary. The pods can accelerate and decelerate relative to the main craft as if the main craft were still. Just as if you are a passenger on an airline and you get up to walk down the isle and back to your seat. You are only feel as if you are moving relative to the plane, not the ground 35,000 feet below.

The situation might change however if the pods moved too far away from the main craft at a right angle and then slowed down relative to it. This may not be the best explanation but I hope it helps.

__________________
"Insignificant molehill sometimes more important than conspicuous mountain." - Charlie Chan