Then, forget everything you know about IT and programming, because the spaghetti like nature of the code in Beat Buddy Manager makes it unfriendly to Users and programmers alike. It is what it is. Until Singular decides to fix it, it is what we have.
I’ll try to address your questions:
Main loops, fills, transitions, intros and outro are midi files. The only real restriction, in my experience, is that they should be made in full measure increments. And, to avoid problems, there should be a note that ends at the very end of the last measure of the part. Typically I address this by dragging a kick drum note to the end of the last measure of the part. One does this to avoid a Beat Buddy quirk which sometimes takes the dead empty space at the end of a midi file and moves it to the beginning of the file, thereby screwing up your timing. A single measure main loop works, but I’d recommend a minimum of two measures. This seems to help the BB deal with the “Cue fill” settings options. Also, since you indicate you would be using Logic to make your midi files, before exporting a midi file, move it to the 1st beat of a track. I’m sure somewhere there is a Logic setting that exports just the selected midi region, but when I forget to move a region to the beginning of a track and then export it, I get whatever number of blank measures were in front of that region added to the export.
Transistions - Transitions start in accordance with the selected “cue fill” setting. This is a setting in the BB pedal. The transistion end when you lift from the transition, and the next part starts at its beginning.
How does it handle - Transitions, see above. Accent hits do not affect the track. The accent hit trigger a separate wav file which plays concurrent with the track.
GM standard - Singular made kits, except for the Latin kits follow GM standards. However, even the Singular kits that follow GM standards do not provide complete mapping of GM drums. This is due to limitation of 100mb of samples per kit. In general, Singular kits do not have the kick drum2 at 35, the 2nd snare at 40, low tom at 41, splash at 55, vibraslap at 58, and Latin pieces from 60 and up. When working with kits, its best to check the mapping of the kit. This can be done via Beat Buddy Manager, by double clicking on the kit name in the Drum sets list, wich opens the Drumset Maker window. You can then scroll up and down to see which pieces are included and where they are mapped. User kits can vary, although most of us try to stay to the GM standard for drums from 35 through 59.
Logic drum kits tend to add pieces below 35. Take note of those and move the drum hits to a supported note.
BIG ANSWER: You don’t. Let BB Manager handle where it puts stuff. If you much about in the BB Workspace you’ll crash it and potentially lost data. You are warned! When you synchronize (and most times on Mac, the option is greyed out) your project file from your BB Workspace is copied to your SD card. Since this is frequently greyed out on Mac, use File>Export Project> to SD card. this process will take several minutes. I run a 12 core Mac Pro dual Xeon with 64GB of RAM, And it often takes 10 minutes or more to finish my export. But, my Project is huge.
Sample rate - 16 or 24 bit at 44.1khz.
Drumkit limit - This is determined by the size of your SD card. I use 32GB class 10 cards. 32GB is the largest card that BB allows. For sake of argument, lets just say I have around 150 drumkits in my project, and over 2000 songs. The BB takes a few moments to boot that up, but its not excessive.