See the page on Publishing Data through the Data Commons.
All data on the CyVerse Data Store are indexed using ElasticSearch. There is an advanced search interface in the Discovery Environment, which will return results for all data you have permission to see (your own data, data shared with you, and public data). There is a simple search interface in the Data Commons, which will return results from all public data in the /iplant/home/shared directory, that is, all data in the Data Commons.
The best way to make your data more discoverable is to use metadata. If you publish data with a DOI through the Data Commons, you are required to add the DataCite metadata template, but you can also add custom metadata. If you are the owner of a Community Released Data folder, you are required to add the Dublin Core metadata template to the parent folder, but you should also add it to any relevant sub-folders.