To upgrade the skill mold chakra will need collect some flowers or fabricate things.
You gain Mold Chakra skill experience with each things fabricated and flowers cuted.

You can buy those flowers with Ino NPC in Konoha.

When you have at last 10 flower, go to the medicinal lab and use the table to craft chakra pill or health roll.

As the amount of your skill mold chakra, the amount of your manufacture will increase, the strength of the created pills will increase, you will be able to walk in the water, and will also improve some jutsus.