1A) With Cut3D you can open & work with your own 3D files as long as the extension for the file is supported by Cut3D.
1B) With 3D-Machinist you can only open & work with V3M models that are bought on the VectorArt3d website, I think that's the only supported extension for that program. That's why the program is free, they make money from the 3D files, not the software to open them.STL STL Mesh files - binary & ascii
3DS 3D Studio - binary & ascii
DXF AutoCAD 3D DXF
SBP ShopBot Digital Probe files
TXT MaxNC Digital Probe
V3M Vector Art 3D files
You can open V3M files in both Cut3D & 3D-Machinist.
2) For Roughing use a larger tool (endmill/ballnose), for finishing I would use a smaller ballnose, but that all depends on the job.
A lot of info is used to calculate the cutting files (Material, Roughing Tool, Finishing Tool, Tool Stepover, etc...). That's what is so good about the Vectric Software, you can change things as often as you want & see what any tool will look like before the cutting. If the tool isn't cleaning up enough, use a smaller tool (ballnose) & a smaller stepover, just remember that by doing so will increase your cutting times (sometimes by hours), again Cut3D will give you an estimate on how long that specific file will take to cut with your selected tool/stepover.
3) You can create your own 3D files for Cut3D in programs, like below. The only one I've used is Silo, it's got a learning curve, If you look thru the Silo Gallery, you will be amazed at how talented some of the users are.