My unsophisticated understanding is that the Cleansweep digital signal processor connects to the factory head speaker outputs and strips away/removes the pre-set factory equalization to provide a "clean" signal to the 5 channel amplifier, which in turn provides signals/power to the 4 speakers and subwoofer. BTW, I also upgraded the rear speakers to Alpine SPS-610s and btw the Focals sound great, clear vocals and mid range with no distortion at higher volumes (note the door sound matting reduces reverberations). These Crutchfield links provide better explanations:
http://www.crutchfield.com/learn/learningcenter/car/factory/upgrade_video2.html
http://www.crutchfield.com/S-9vbxIKqbcuH/learn/learningcenter/factory/sound_processors.html
http://www.crutchfield.com/S-BO6vjMunbh6/learn/2006-2012-toyota-rav4.html (note suggestion to replace stereo and not factory amplifier is probably more applicable to non-EV RAV4s without the integrated stereo/NAV touchscreen unit)
Regarding the question on most bang for the buck/least trouble audio upgrade, I can't speak firsthand since I had the complete upgrade done (although I went into the audio shop thinking ~$300 speaker upgrade was enough and walked out $1500 lighter lol). The RAV4 owner in the link below seemed to think the most bang for the buck is clearly upgrading speakers (esp. if you go with the Focals and sound deadening in the doors). The 4 speakers + noise dampening cost about $600 in my case. FYI, the amp was ~ $430, DSP ~ $220, subwoofer ~$120, labor ~$150 (including soundproofing). Bought the equipment and had it installed at Advanced Car Creations in Garden Grove (4.5 stars on Yelp) - they did a great job and were competitive with their pricing.
http://www.rav4world.com/forums/124-4-4-interior/119242-250-gives-great-sound-improvement.html
