I run SPB 3.5, and indeed it doesn't work together. Sense is being inactivated as you install SPB. But you can access quite a few HTC apps still. Just by looking for them in the windows map on your device, you can also manually add shortcuts to them in SPB.
Examples of apps that do work:
- Video camera
- Footcam (of the footprints suite, though this doesn't work completely well...)
Apps that do not work:
- Audio manager
I just use different software for audio, footprints I won't use at least in the near future.