Assuming you set everything correctly, this means the switch on the back for the RCA’s is set to main not booth, any RCA to mini-jack cable should do (providing it is a regular left+right RCA to stereo mini-jack).
It makes complete sense that you get headphone cues only when using the S2 for sound. Sometimes (not sure no Traktor anymore as I ditched it years ago) you can set the software so that main sound goes to one place (speakers through PC out) and headphones to your S2 for cueing. Still not an optimal way to go, not in the least because you can end up with different latencies.
The other thing that is wise to do, is to disconnect the Bose from USB so the only connection is the aux in on the control pad.
For testing purposes you an of course eliminate the cable as source by trying another one.
Also you can try borrowing a pair of active monitor speakers and hooking those up with the Bose fully disconnected and turned off. That would eliminate the Bose as source if you still have those noises.
Personally I am no fan of using movie/gaming PC speakers for DJ-ing, period. Too often not a good match. Also price-wise you don’t have to. A pair of KRK 6s will run you about 270 euro as opposed to 400 for the Bose. And you can hook them up with balanced Jack-Jack cables which should normally eliminate any cable induced problems.
Should you need speakers that handle your other PC sound needs too, then I could suggest the Yamaha AG06 mixer. It has a built-in sound card, RCA’s for your RCA-RCA controller connection, an extra aux in (should you like to hook up iPad/iPhone or something) and lot’s of other features. If you play out in the future, it will be great for hooking up balanced PA speakers. You also get volume control right on your desktop. I have one sitting on my desk (well the smaller AG03) and I plug in my controller to the aux and my KRKs are connected Jack-Jack balanced.
Just my 3 cents as usual.
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