In BB v0.76 you can either directly set the bone index of your extra bone in the properties window or right click the bone and choose "move to the end of bone array" (which you want to do for extra bones). And if you want to reset all bone indices to be in order you can choose "regenerate bone array".
So for any bones you add that aren't present in a vanilla structure, you just open a complete character .pac in BrawlBox 0.76, find the new bones, right-click them, and go "move to the end of bone array"?
And this allows addition of bones to be wifi-compatible (as long as hit boxes aren't modified) and these bones can be animated without the use of a PSA edit?
Is there's a certain order you need to move bones to the end of the array when dealing with child and parent nodes? ie. Move the children down first, then their parents and work your way up?