Splitting stl files into multiple pieces to 3D print in multi color

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So recently, I gained access to a prusa 3d printer with a multi color addon, allowing for like 6-7 different colors to be used in a single print
Issue is, making files that can utilize this
I looked online and meshmixer seemed like the best bet, so I download it, run it, and import, say, a train I made in fusion360
I try and follow the work flow of those I see online, and do the selection, boundary thing, and create face group several times for different parts
Issues start when I do generate complex
When I do that, the boundary line things dont appear, wont be selected, or just dont exsist and I dont know why, but it prevents it from seperating the sections I want it to, and overall has just been a mess(yesterday I spent around 4 hours trying to seperate a L from a coin thingy, the line surrounding it was red, and I couldnt figure out why)
If anyone can help, or reccomend a program more built for what I need, please let me know, as this is getting very frustrating
also if I do accept the generate complex(the offset thing is annoying though, as the first few times it like half split the stuff I wanted it to, but left a random jumble of faces behind, which should have been part of the split piece), and then I split complex,
Thanks!