I have a part with a flat base perfect for placing directly on the bed. How do I place the part directly on the print bed? With no gap so bottom of the part is exactly mating with the print bed?
After you import the STL, you should just need to hit the "Arrange" button in Creator. It will center the part and align the bottom of the part (as it sees it) with the surface of the bed. Can also try the "Drop" button. Perhaps run the model through some of the checks to make sure it is manifold, no lurking goofy-triangles, etc. will help...
I use OpenSCAD, and even parts that extend below Z=0 in the CAD file (centered on Z=0 rather than building up from Z=0) drop properly in Creator and print flat on the bed...