Assuming you have downloaded the Ketryx Connector app from Atlassian Marketplace, Ketryx configurations and schemes (ex. Ketryx Risk screen, Ketryx standard workflow, Ketryx issue type scheme, Ketryx issue types) will be applied to Jira projects based on the following characteristics: 

• If a company-managed Jira project contains 0 items and the "Use Ketryx issue types, screens and workflows" Ketryx scheme is selected when creating a new project in Ketryx, Ketryx configurations, schemes, and custom fields will be pushed into the empty Jira project.
• If a company-managed Jira project contains >0 items and the "Use Ketryx issue types, screens and workflows" Ketryx scheme is selected when creating a new project in Ketryx, Ketryx schemes and workflows will be pushed to the instance (in the background) but not applied to the Jira project. The project will keep existing settings until the schemes are manually applied to the Jira projects in Jira. 

Note: Applying Ketryx schemes to a project may cause global configuration changes (to issue type icon or name) if a conflict exists between Issues Type Names in the instance and Ketryx default item types. We therefore recommend reviewing Issue Type Names in the Jira Instance and de-conflict any Issue Type Names that overlap with Ketryx default item types, prior to connecting Ketryx to any Jira project. 

To deconflict an issue type, first create a new issue type in Jira (using the name you want to switch the Ketryx default to), and then use the Item type names advanced setting to rename the Ketryx default to that name.