You actually can't plant the seeds yourself, you have to make your Chao do it for you. If one of your Chao wins the Crab Pool race, they get a small shovel as a reward; likewise, the reward for the Stump Valley race is a little watering can. Make sure you have a Chao that has won both of these items. Then hand the seed you want to plant to that Chao, and the Chao will plant the seed for you.
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You need a shovel and a seed and give the chao the seed and eventually the chao will find a spot to plant the seed
Shovels and watering cans can be won more than once so don't worry. Also you only need a shovel because the watering can only speeds up the growing speed. It also makes the tree live longer.
You plant an unrare moshling seed which then depending on the seed will soon come into a moshiling
Its a PLANT POKEMON, technically a seed
Cosmo died because Tails had to kill her with a cannon he had no choice =[ however, in the Japaneese, when sonic returns to the tyfoone and gives the seed to Tails, Tails says "It´s not true. Just a second ago this was Cosmo" so if you are going acording to the japaneese version she was turned into that seed