dencol
I prefer submixing BFD2 tracks (mono kick, mono snare, stero toms, stereo cymbal, etc) then assigning each sub to an audio input tracks in Sonar. All driven by one midi BDF2 instrument track in Sonar... Best of both worlds.
Oh... One other thing I learned the hard way, never export using Quick bounce. Let the song play out while exporting. I've experience sync problems and note drops n BFD tracks... Don't know if this happens with anyone else.
With regards to your quick bounce problem, have you tried enabling off line mode in BFD2 and has it made any difference?
As for the mixing question pro's and con's
Pro's BF2 mixer is excellent and in my opinion it's better in some ways than sonar's. At the time of it's initial release in 2007 the bundled effects were very much better than those included in sonar and as good as many high end effects that would cost an arm and a leg. But that was 5 years ago. In terms of sound there is really no difference if you have BFD2 routed to a stereo master out in sonar or you're routing each channel, kick, snare etc to mono outputs in sonar.
Cons, I wouldn't recommend routing BFD2 to separate outputs unless you are wanting to use third party effects but aside from your third party effects being more to your liking than the BFD2 bundle they are much easier to automate.
Having said that you can automate all 501 of BFD2's parameters from kit piece tuning to any of the included effects. It's just a little more time consuming but quite easy once you know how.
I actually have most of my tracks in BFD2 routed to individual channels purely on the off chance that I might use third party effects so for that reason it might be a good idea to do that.
Whatever you do it's always a really good idea to save your different routings as templates. On that note I have some (amusing) BFD2 templates that I posted some time ago to help new users understand how it was done.
They also include a loop and the kick drum has automated tuning as well as being laden with effects but don't klet that distract you from the main purpose, I just got bored
The ones that are routed to a single stereo channel are named BFD2 (kit name) master.
Sorry Beepster, didn't do any for BFD Eco

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You can find them here
BFD2 templates Cheers
Steve
P.S. The first 2 presets are for my favourite "cocktail expansion kit" so if you don't have that it won't work.
Also if you don't have it and you've got the money I can't recommend it highly enough, really bright and versatile and right now is only £18 ($25) which is a bargain.