If you look at the XYZ axis directions in S3D, you need to make sure those match how you are designing your models in your CAD package. If you design them in your CAD package so that the Y-axis is upwards, then it's going to import sideways when you try to 3D print the part, since the Z axis is always upwards on a 3D printer. So if you model them in the correct way, then this shouldn't happen.
However, if you have lots of models that are already incorrect, you may want to look at the import actions which can automatically reposition and rotate the parts for you:
https://www.youtube.com/watch?v=E8ytvwfCn5g