OK, after all this I believe I've found a solution to my problem!
I got an idea after I realized that since my speaker and receiver are inseparable, that it must know to roll off the bass frequencies to the subwoofer automatically. So I tried (from the Pioneer side) setting all my speakers to "large" even though they aren't full range and the subwoofer to "on". From what I can gather, this is sending all the possible bass information from the Pioneer to my Logitech. I figured my Logitech must be sending the proper information to my sub because it's now outputting way more bass than it did with the speakers set to "small" on the Pioneer.
This leads me to believe that the Pioneer's "bass management" isn't really managing much of anything. I figured setting the speakers to "small" would roll off the bass frequencies to the LFE channel, but what it actually feels like is it's just attenuating the bass frequencies for the satellites.
I know the Logitech Z-5500 isn't exactly ideal for SACD listening but at least I can now hear my favo
urite albums in uncompressed 5.1 which is what I was going for. Again, I'm sort of new at this so if anyone can revise my setup or give me any additions tips/info, it would be greatly appreciated. Everyone has been nice and informative so far, I'm glad I was able to sort out this problem.
Eventually I'll be adding an HDMI receiver to the mix so I can enjoy pure DSD but until then, this seems to do the trick. Thanks for the responses, everyone.