Motor oil will be a total loss system via petroil or oil injection but the transmission will require filling or maintaining at the correct level with the correct type and grade of oil.
Unlikely there is two filler plugs. Likely one plug is the filler and the other is the level plug - the lower of the two. Remove both plugs and ensure the bike is level and trickle oil into the higher of the two holes until it begins to drip from the lower hole.
If there is doubt then completely drain the transmission and refill with the correct amount.
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