公共职员在超市进行了调查 sentence order
Your sentence 在超市公共职员进行调查了 is ok. It's better you put a comma: 在超市，公共职员进行调查了. But logically, 公共职员在超市进行了调查 sounds better. You can split it like: 公共职员在超市/进行了/调查. The first part 公共职员在超市 talks about: 公共职员 is in supermarket; The second part talks about the action 进行了; The third part talks about the target of the verb: 调查; 

As for 进行了调查 vs 进行调查了, 进行调查了 takes 进行调查 together as a verbal phrase while 进行了调查 separates it into two words 进行 and 调查. 进行了调查 put an emphasis on the word 调查, which is what 公共职员 have done in the supermarket. 

Hope this clear.