The rules state a cube can be picked up and moved out of a starting position by the “driver” but it does not indicate whether the cube has to be in the starting position that the “driver” is trying to place the robot into or does it mean you can move the cube if it is occupying any of the two starting positions?
Autonomous Starting Position - Cube considered in Starting Position even though Robot not starting in that position
Please review the Q&A Usage Guidelines, specifically point 3, "Quote the applicable rule from the latest version of the manual in your question.".
Although the question does not explicitly state it, the title reads "Autonomous Starting Position", so we are assuming that you are referring to a Programming Skills Match. In that case, this would be governed by rule RSC5, quoted below with a portion bolded for emphasis.
<RSC5> A Team may handle their Robot as many times as desired during a Programming Skills Match.
a. Upon handling the Robot, it must be immediately brought back to any legal Starting Position.
i. Driver may reset or adjust the Robot as desired from this position, including pressing buttons on the Robot Brain or activating sensors.
b. Any Game Objects being controlled by the Robot while being handled must be removed from the Robot and gently placed in a non-Scored position by the Team.
c. Any Game Object in the Starting Position may be moved out of the Starting Position and gently placed into a non-Scored position by the Team.
d. During a Programming Skills Match, Drivers may move freely around the Field, and are not restricted to the Driver Station when not handling their Robot.
i. An intent of this exception is to permit Drivers who wish to “stage” Robot handling during a Programming Skills Match to do so without excessive running back and forth to the Driver Station.
Note: This rule only applies to Programming Skills Matches. Driving Skills Matches are still governed by <G17>, especially for strategic violations.
Part C is intended to refer to the Starting Position that the Robot is being brought back to. Cubes in the other Starting Position would not be included in this exception.