I use Cubase SX and BFD. I use BFD as a vst plugin. When you save a project that includes BFD as a vst, the BFD setup is saved along with the Cubase project. Here's how I set it up:
Devices, VST Instruments, click on an empty slot, choose BFD Stereo, Group, or All, your choice. For messing around and songwriting, I use BFD Stereo, which is just a stereo output from BFD to Cubase. For more control, I use BFD All, which outputs all BFD channels to Cubase allowing you to apply audio effects to each individual drum mic. All direct drum mics in BFD have pan controls so getting your tom rolls to go across the stereo field should be simple enough to figure out.
Add a MIDI track. For the output of the MIDI track, choose BFD. If you have a MIDI controller hooked up, choose it as the MIDI input, if that's what you want. Or, you can use the Groove Library patterns from BFD. Make sure that MIDI out is enabled in BFD if you use the Groove Library patterns.
Load a kit up in BFD. If you're using the Groove Librarian, load up some patterns.
If you get clicks/pops, cutting out, etc., try switching to 16 bit mode and/or changing the cache sizes in BFD's options. Also, unload any kit pieces that you are'nt using. Check out BFD's options in the manual.
As far as getting a natural sound, I try to approach it like a real kit. I pull all faders down in BFD except the overheads. I try to get a good sound by adjusting each drum channels individual trim fader. Then, I start bringing up the direct mic faders as needed. Now I'll play around with eq/compression in Cubase to tame peaks and carve the sounds a bit. After I have a sound I like I'll record a drum track. If I need more ambience, I'll start bringing up room and/or pzm faders.
Hope this helps a little. Check out the manual to learn how about BFD's options.
