How do I park secure.primary.com on top of the multisite ID:1 domain: www.primary.com (primary multisite domain)

Install WordPress MU Domain MappingPlugin, and edit the wp_domain_mapping database table.

Insert a new row for blog_id #1 manually, for example:

 +------+-----------+----------------------+----------+
 |  id  |  blog_id  |  domain              |  active  |
 +------+-----------+----------------------+----------+
 |  5   |  1        |  secure.primary.com  |  1       |
 +------+-----------+----------------------+----------+

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