Hi Justin,
I just saw this thread so thought will share some of my experiences with you.
I have a KRP600A, which has a separate media box with 4 HDMI input sockets and BSYS3 but the 2 systems are incompatible when one starts using HDMI. Currently, I connect all audio - BS9000 via ML to the BSYS3 and my Pioneer LX91 BDP audio via Coaxial to BSYS3. I use BL5s as front speakers, a pair of BL3 as centre and another pair of BL3 for rear.
For video, DVT is from BSYS3 with DVI to HDMI into the Pioneer media box and the LX91 video via HDMI into the Pioneer media box as well. The KRP600 screen is connected to the media box with the new cable format called DisplayPort.
The picture quality is incredible as Steve of Sounds Heavenly stated, 'been blown away'
For remote control, I use both Beo4 and 5 and I have just ordered a Lintronic TT455-RT-238 universal signal converter (as kindly suggested by our Aussie forum member Corvin) to convert both the Pioneer KRP600 and the LX91 IR signal so that I can use the Beo4 and 5 to control the Pioneers.
In you case, I suggest you should consider getting a Pioneer AV amp such as the SC-LX71. You could connect your KRP500M seemlessly into the SC-LX71 via HDMI. If you only want to have stereo sound for the time being but retaining the BL3 speakers, these speakers can be connected to the pre-out on the SC-LX71. Yo can also connect your BS9000 into the SC-LX71 via SPD/IF (coaxial).
Steve of Sounds Heavenly can custom make the BL3 cables (RCA to Powelink) and also the SPD/IF cable. The volume on the BL3 can be controlled via the volume control on the SC-LX71. However, you would need to use the Beo4/5 to control your BS9000 such as loading of CD and pre-set output volume on the BS9000.
At one stage, I was considering ditching the Bsys3 but after talking to various forum members, as I have BL5s for front and it has its own volume control, the use of SC-LX 71 is not that straight forward. Couple with a good offer from my dealer, I have decided to retain the Bsys3.
I am very happy with the set up since I think for the video - I only watch Blu-Ray DVDs, it is better to pass the video signal directly from my LX91 player into the pioneer media box thereby negating the need to use the Bsys3 for intermediate processing.
Once I have the Lintronic set up, I could then use the Bo4/5 to control all the equipments.
If you are interested in the Pioneer AV, check it out on
http://www.1ststopav.com/ and they are very helpful bunch. Below you will see the link to the rear view of the SC-LX71.
http://www.avland.co.uk/pioneer/sclx71/rearlrg.jpg
I hope this helps
KC