Word order question. Describing a rabbit's eyes
... the "How" of the main verb in the sentence should always come before the verb itself.


This is correct if "how" is referring to the adverbs. In Chinese, adverbs are placed before verbs, unlike in English they can be either before or after.


  It's eyes were red, like a pair of rubies." (它的眼睛红红的，像一对红宝石)


The thing with this sentence that makes it easily mistaken is there are two verb clauses:


were red. (是)红红的
like a pair of rubies. 像一对红宝石


The structure is quite obvious in its English version. But in the Chinese version, copula 是 is omitted before adjective 红红的, making it ambiguous to learners or even native speakers.

Hence, #2 is not "how" or adverbial for #1, but another verb clause. The order of the two verb clauses should be dictated by the semantics, not syntax or grammar. Since one clause is direct description and the other is analogy, there is no right or wrong on the order.