It is rarely clear which way to put the film in a film scanner. The trivial answer is that if the image comes out mirror reversed or upside down, then turn the film over, maybe in two directions, and remember which way that was.
The emulsion side has a dull surface, which is very apparent in Kodachrome or B&W film, but it's hard to detect much difference in most color film. Often it's easier to judge the sharpness or dullness of reflections from the film surface than to see a difference in the actual film surface itself. The writing along the filmstrip edge will be reversed if you are looking at the emulsion side. However, a mounted Kodak slide will have the Kodak logo on the emulsion side. The image will view correctly from back side, or will be mirror reversed if viewed from the emulsion side.
In a film scanner, it is not so clear how the film should be oriented to come out right. The Minolta Scan Dual II has very clear instructions, it says the emulsion side goes up, but the image comes out mirror reversed. Most such film software provides controls to rotate and/or flip the image if it's wrong. Or you can turn the film over and scan it again. Or you can ignore it until later.
Most film scanners only have enough CCD cells to cover the short side of the film, so there is no choice of portrait or landscape orientation, and a filmstrip holder only has one direction anyway. Mounted slides must be oriented the same as filmstrips, even if they fit the other way in their square holder. The preview software can rotate the images for this reason, and some frames will be both ways. You will probably grow accustomed to viewing it sideways, it really doesn't matter much while scanning. You can always rotate it later in the photo editor.