I really can't understand... "Decrypt9 boots a little faster": placebo, or show that two ifs and ors slow things down in a measurable wayNo version has payload files. They are optional. I don't use any. Of course, I'm using BootCTR9 defaulted to Luma3DS. Decrypt9 boots a little faster, I can hotkey over features I don't use, etc. Besides, I'm a firm believer in having an app that does one thing and does it well (especially if it's going to be the first thing that runs).
There's no right or wrong way to set them up. You can place whatever wherever you want it. I like having Decrypt9 on up, Godmode9 on down, EmuNAND9 on left, Uncart on right, ReiNand on X, and Cakes on Y. But that's me. Note that you'll have to cut off the first 12000 hex bytes of the Cakes.dat file (easiest way is to load it in a hex editor, hit Ctrl-G, tell it to go to 12000 hex, hold shift, hit end, goto File, New, paste, then save it) and save it as something like "y_Cakes.bin" i.e. you want to run that from the Y button. Almost everything else comes with an "arm9loaderhax.bin" that can just be renamed (if, for example, I did want to use Luma to launch Decrypt9, I'd simply copy the "arm9loaderhax.bin" from it to the "payloads" folder and rename it to "up_D9.bin"). I'd say it's a good idea to have a backup plan. You never know when your favorite CFW will break something (case in point, DS mode not working in 5.4 on O3DS) and you might need to use something else temporarily for that until they get it fixed.
You shouldn't have needed a firmware.bin just to get it to run. Maybe your EmuNAND isn't completely updated (or your SysNAND wasn't completely downgraded if it's a fresh EmuNAND install) and is running a mix of files from different firmwares? Oh well, it won't matter once you have A9LH installed -- it will be running a fully updated 10.7 after all (except for those firm partitions, of course).
I can hotkey over features I don't use: yes, but this can be also confusing for most other people
I'm a firm believer in having an app that does one thing and does it well (especially if it's going to be the first thing that runs): it's not like chainloading a payload (load into memory, jump to it) is such a tedious task, or requires complicated code... And I promise, it doesn't brick the device.
Also, DS mode works on stable 5.4, there was a derp in a nightly that made it stop working but that's solved by now.