The rules depend on the language from which you are transliterating. Sometimes there are firm rules, sometimes not.
For example, from Mandarin, there has been a formal change. We used to write Mao Tse Tung (Yale system), but we now write Mao Zedong (Pinyin system). The pronunciation has changed accordingly. Some names are more resilient. We still call Kung Fu Tsu 'Confucius'.
From the Russian (cyrillic) alphabet, Tschaikovky has at times been written as Chaikowski, and other variants, and this sometimes changes the pronunciation, even though the original idea is to spell the word as closely as possible to an English version of the pronunciation.
From languages that also use the roman alphabet, English will sometimes retain the original pronunciation, but usually only if the phonemes are already used in English. For example, not many English speakers would pronounce the double consonants in the Italian words cappuccino or mozzarella. Many French words and phrase do retain their original pronunciation. Perhaps French has a certain, er... je ne sais qua.
As far as ordering V and C, a sensible rule would be to use only those structures and pronunciations that already exist in English.
But it's a huge topic that you've raised. Do you have any examples that could be dealt with more concretely?