Can I report tax-exempt liabilities for my subsidiary organizations in the Schedule K, Form 990?

No, a liability acquired by your organization shouldn't be reported in your subsidiary organizations. For example, if your organization issued a tax-exempt bond and if it is allocated to a subsidiary organization, then only one organization (either the parent, i.e. (you) or the subsidiary) should report the liability while filing Form 990 Schedule K along with Form 990.
 
Similarly, if a parent organization loans or allocates a tax-exempt bond issue to a group of its subsidiary organizations, only one of the organizations (either the parent or the group of subsidiaries) must report the liability on Schedule K along with Form 990.

If your organization is required to report schedules other than A, B, and G, we recommend choosing our interview-based filing method.