With be verbs, English questions mark the simple past with the main verb. In the question, Where were they?, the verb were is in the simple past. However, with other verbs, only the auxiliary verb is in the simple past. It is used in combination with the main verb.
Consider the question What did you say? The first verb is in the simple past, did. However, the main verb say is not. This pattern is also true for yes-no questions. Consider the example Did she agree? Only the auxiliary verb is in the simple past. The main verb is not in the past tense.
The same structure is used for emphasis. The sentence They went is more emphatic with the structure They did go. In this structure, the auxiliary verb is in the simple past, but the main verb is not.
In English questions with be-verbs, the be-verb is in the simple past. However, with other verbs, English adds an auxiliary verb. This process can be called do-support. The auxiliary verb is in the simple past but the main verb remains in the base form.