Yes, any image with a transparent background that is used for a non-background step will remain transparent.
Please ensure that the image you upload is a .png file, as .jpg files do not support transparency.
Using Photoshop, or the free software - Paint.net (see below), is a great way to get a crisp transparent image for tools, logos, or icons.
SimTutor also supports semi-transparent images, for use cases where what lies below where the tool is important to be seen too. See example below how the saw blade is still visible beneath the spanner.