There are two ways to setup an existing taxonomy into Atlas;
1.) If you have Hive, then run the import-hive.sh utility. This utility scans all of the hive tables and creates the matching Atlas entries. For 2.5.3, you will find the utility at ./2.5.3.0-37/atlas/hook-bin/import-hive.sh
2.) You can also add entries and update properties using the REST API. One article describing this is available at: https://community.hortonworks.com/content/kbentry/74064/add-custom-properties-to-existing-atlas-type...