In both cases above, the question really isn't about diagramming rules, but about syntactical rules. In particular, your question seems to be how we can tell the difference between the subject and the predicate nominative. If we simply followed word order, we would make many, many mistakes, and not only with regard to subject and predicate nominative, but with many other constructions. Note, e.g., John 4:24. Certainly PNEUMA is not the subject, even though it comes first in word order, right? Or how about Hebrews 1:10? Is ERGA the subject because it comes before hOI OURANOI? Or Mark 2:28? Is KURIOS the subject, or hO hUIOS?
As Mithril suggested, I think you would profit by reading Wallace's treatment of this subject in his grammar (pp. 40ff.), especially his treatment of the "pecking order" (pp. 44-46).
The key to distinguishing the subject from the predicate nominative is the general rule that the subject will be the known entity. The known entity (subject) will be distinguished from the predicate nominative in one of three ways: (1) The subject will be a pronoun (except for an interrogative pronoun), whether stated or implied in the verb. (2) The subject will be articular. (3) The subject will be a proper name. The "pecking order" comes into play if both the subject AND the predicate nominative possess one of these three tags. I'll let you read Wallace's treatment when you get a chance, and I'll comment briefly on the two examples you give.
First, John 1:1. So which of the nominatives is the known entity here in the third clause? It is clearly hO LOGOS, since we find it expressed already in the first two clauses. In both cases it is the subject of the respective clause and there are no predicate nominatives to challenge it as the subject. It is already the known entity by the time we reach the third clause, and it has the article, so it is the subject. QEOS is explicative of hO LOGOS, the known entity, not vice versa. Often words are fronted in a clause for emphasis, which I believe is the case with QEOS here. See also Wallace's discussion of subset propositions on p. 45.
Second, 2 John 7: Once again, we must determine the known entity. That would be hOUTOS, since it refers back to the previously introduced hOI hOMOLOGOUNTES. So hO PLANOS and hO ANTICRISTOS are not the known entity, but rather explicate hOUTOS and its antecedent, hOI hOMOLOGOUNTES. The reason that a pronoun will be the subject is that it will normally refer to an entity already known. Wallace notes that personal, demonstrative, and relative pronouns function as the subject because they are a substitute for something already revealed in the context (a known quantity).
Hope this helps,