In the paragraph El uso del Presente de Subjuntivo you have learned when to use the subjunctive. In all the examples the main verb was in present tense and all the verbs in the subordinate clauses were in present subjunctive:

Quiero que venga Juan. (I want Juan to come.)

In order to make this decision you have to answer two questions:

1. What is the tense of the main verb (the verb in the main clause)? 
2. When did the action of the subordinate clause occur in relation to the time frame of the main clause?

• when the verb in the main clause is in imperfect and preterite and the action of the subordinate clause happens before the action or time frame of the main clause:

Ayer quería que Juan hubiera venido . (Yesderday I wanted that Juan had come.)

• when the verb in the main clause is in present tense and when the content of the subordinated clase is a description (with no specified beginning or end) in the past:

Dudo que el pescado hubiera dicho algo antes de morir. (I doubt that the fish had said something before it died.)

• in "if clauses" that refer to a situation contrary to past reality:

Si hubiera tenido dinero, habría ido al cine. (If I had had money, I would have gone to the movies.) (I didn't have  money [past truth]. If this had not been true, I would have gone to the movies.)

In this kind of "if clause" you have to use the pluperfect subjunctive after "si" and the Past Conditional in the main clause.

• in wishes for the past introduced by "Ojalá" :

Ojalá que hubiera venido Juan. (I wish Juan had come.)