Combining .STL files

[MagicEngineer]

I have been trying to do this tonight and I keep getting "fatal unknown fault........." when it's finished making the hole and I hit the accept button.

That happens when there are problems in the mesh that it can't get past. When the boolean functions result in all involved pieces turning a deep red there are issues that must be addressed, typically resulting in a non-manifold solid. Usually you will see a red or blue line extending from where the problems exist. This is the part that comes with experience. sometimes a small movement, or resize fixes the issue. Sometimes a piece might require a bit of material being removed where the parts overlap. Sometimes it only requires making solid again at a new resolution. I almost quit using Meshmixer for exactly what you are experiencing, but after hours of practice I have developed a better understanding of its quirks and actually enjoy using it. I just played with your files, and in this case the issue is that the bee is in more than one piece and is an easy fix. Select the bee object. Then go to edit>separate shells. This will break it up into two parts, the bee and the "GT". Now do the the boolean difference function with each part individually.

[theboz1419]

Yeah, I was able to get by the fault, but I'm looking at doing something different after playing around with it. What I want is that the parts that get cut out, needs to be black. I tried to print a yellow case with the bee logo, then I made a black abs slurry and filled inbetween the parts that were printed. It did not work that great, as it is a pain to get it off the build plate without making some distortion in the logo and case. I thinking about trying to do material swaps(black and yellow) and make sd3 think I have a dual extruder. I saw a how-to on hackaday. Or I might just give up and just give my customer a regular old case, easier that way, lol.

[MagicEngineer]

I tried to print a yellow case with the bee logo, then I made a black abs slurry and filled inbetween the parts that were printed. It did not work that great,

I know it's not what you had in mind, but you could always fill the cut out with black paint. A wipe on wipe off technique is easy. Another technique I use in a case like this, to avoid the rough finish left by a bridging layer, is to slice about a 1/16 of an inch off the top of the case. (plane cut>keep both pieces then separate shells) Cut the bee out of that piece all the way through. Then print in two pieces. You can then throw a quick spraying of paint where the bee will be and laminate the pieces back together. The result will be a black bee cut out with a nice crisp line between the black back and yellow sides.