I believe that Section 7: The Game can help provide you the answer.
Quote:
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<G09> BALL Starting Positions – Prior to the MATCH, each ALLIANCE is provided with six BALLS to be placed on the FIELD. The BALLS must be placed on a STARTING GRID location prior to the MATCH start. When the FIELD is viewed from the ALLIANCE STATION, the BALLS must be placed on the right side of the CENTER LINE, with one BALL in the near ZONE, two BALLS in the MIDFIELD, and three BALLS in the far ZONE. The BALLS must not be in contact with a ROBOT at the start of the MATCH.
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So this means that yes, your team is allowed to decide where the balls are placed on the field prior to the match.