I'm sorry, i'm not able to understand from your question where exactly you are facing the problem. If you wish to use SequenceFiles through Hive you just have to add STORED AS SEQUENCEFILE clause while issuing CREATE TABLE(most probably you already know this, nothing new). When you work on SequenceFiles Hive treats each key/value pair of the SequenceFiles similar to rows in normal files. Important thing here is that keys will be ignored. Apart from that nothing very special.
Having said that, if you wish to read both keys and values, you might have to write a custom InputFormat that can read both keys and values. See this project for example. It allows us to access data stored in a SequenceFile's key.
Also, if your keys and values are custom classes, you will require to write a SerDe as well to serialize and deserialize your data.
HTH
P.S. : I don't know if this is exactly what you were looking for. Do let me know if it is not and add some more detail to your question. I'll try addressing that.