It isn't confusing to me, but that is because I only know from doing it. I don't like to read words on how to do something. I'll read the Cubase manual or a Reaktor manual when I must, but I'm not built to read manuals or technical writing. I had to read the Vienna Instruments manual to get any handle on dimensions, but I think a video is clearer to me, and I think the VSL tutorials are quite good.
Here's how I use BFD in VEP: my preferences in BFD2 are 'load nothing on startup'. However, I save everything as a preset, which is mixer and mapping, everything. I let VEP remember what kit is in what project, it loads that kit.
(By project, or 'instance' I mean a vi frame. One or more vi frames reside in a metaframe. I definitely save the BFD2 vi frames/projects with a descriptive title that starts with "BFD". I keep BFD2 separated, it's a 32-bit and it uses memory, and it's a fancy GUI, and fancy GUIs don't play so well with other fancy GUIs inside VEP. Such as, Kore 2 and BFD2 in one vi frame is problems waiting to happen.)
I am using both 32 and 64-bit servers, so yes I'm saving both. I have run into trouble with older projects where I used a different M.O., VEP coupled with Cubase, and returning to remix a project (after I changed and screwed up, saved it as decoupled, now it loaded empty instances) I ended up having to find the vi frames, which fortunately I'm somewhat careful to save.
Now, I always run decoupled, preserved and save diligently, yes. I master my own audio, and I have had to go back with say a too-hot master and sort it (and I'll come back to mixes) so I have to be observant in my methodology. I make mistakes so I have to cover myself.
Edit: the value of decoupled and preserved shows when say, Cubase crashes or hangs and I force quit; this is very rare for me, BUT... let's say I got so involved with the thing I neglected to save on the VEP slave. It's still there, I don't have two problems but one.
I would advise making copies variously as you go, as sometimes a vi frame, a channel set, a metaframe even becomes corrupt, I guess from a hot computer (I'm running mine into the ground I think).