You need to head straight to the FAQ and read up on the Dynamic EQ Reference Level Offset parameter. What you are experiencing is overblown bass and surround volume that's common with DEQ and non reference (film) content. The DEQ Ref Offset allows you to tone down the boosts and tune it to the content. Most receivers memorize this by source.
If you boost the sub and use DEQ then yes you are double boosting. If you want to use DEQ then put the sub back down and experiment from there.
I personally set mine to -10 as -5 and 0 just seem to bloat the bass.