Funny you should ask. I spent some time last weekend making some custom cables for a pair of REL subs I just bought. The subs are to the outside and just a bit behind my speakers, so it made sense to make a short cable to hook up to my speakers, not the amp.
The result? Dead silence, no humm, great integration.
And , yes, the manual is very poorly written (or NOT written) for stereo subs! Good grief REL. You can do better.