The "best" way is to manually apply traps (overprints) to the objects as they are created. Then, if the objects are moved, etc., the traps will be retained, eliminating the need for retrapping the file. This usually is the best policy for files that may be reused and picked up again and again with only small changes. A close second is using Deskpack plugin for Illust which adds a layer with the overprints. The only disadvantage to this is that if anything is edited, the trap layer has to be considered.
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