"Are the boxes supposed to make holes in the base shape or protrusions?"
No the boxes should just the in place and printed as is ...maybe when I did the merge it did mess it up even more :/

Attached pic is a Boolean merge with line to split is the way I do it to split my model ...with simpler items no issues..with other things abit more complex I always have an issue :/


This should be one before split in the middle.
All the ones I have , have the boxes already.
Thanks you!