Custom fields are supported for the Atlassian Connector for Eclipse. However, the following limitations apply:

• Custom fields are not displayed in the task editor when creating new issues. This can cause issue creation to fail if custom fields are mandatory.
• Custom fields that are specific to a workflow state, e.g. are only displayed when resolving an issue, are not displayed in the task editor. This can cause a workflow transition to fail if custom fields are mandatory.
• Multi-select fields are not supported and not displayed in the task editor.

See this issue for additional information (please vote the issue and watch it to get notification about status updates).