Where - were

Where is a conjunction, relative pronoun, or an interrogative depending on its grammatical context. Its general meaning is of place ~ 'in which place'.

were is the plural form of the past tense of the verb 'to be.'

It is correct, and makes sense, to spell the common question as: Where were you? /WewE?u:/. It makes no sense at all to spell it: Were where you? /wEWe?u:/.

(If you are interested in language, you may care to observe that the changes in the consonants change the pronunciation of the vowels that follow them.)