Both are used along with another action or time reference. In that sort of sentence, past perfect describes an action that happens first. The other action would take place at the end of those 3 years and it implies that he was still working for that company after the other action.
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egerol1the difference between past perfect continous and past continous.There are so many uses of each of the tenses of English that it would be impossible in a single post to give you all the differences, even for just two of them. Let's just concentrate on the two sentences you wrote.