Visible crew/equipment: In Servo's room, Trace Beaulieu's hand is very visible operating Crow. Watch the bottom of frame when Crow approaches the Interocitor and says "Well, let's see what this baby can do." (00:48:00)
Visible crew/equipment: In the beginning, when Crow is digging a hole in the satellite's hull, there are several scenes where puppeteer Trace Beaulieu is visible within the hole, operating Crow.
Visible crew/equipment: During shots of the Satellite of Love orbiting Earth, it is possible to see the wires holding up the satellite on either end of the ship.
Chosen answer: They sit in front of a big screen -- or rather Joel or Mike sat. The puppeteers crouch down below the row of seats and hold up special black puppets to project the silhouettes. They did do takes for segments of the movies. I imagine it would be painful for the puppeteers to crouch for 90 minutes!
Carl Fink