Single magnets do work fine with the linear motor track, but lack any directional control - whatever you have stuck on top will point in unpredictable directions. Two magnets (one flipped so that you have a north and a south pair) will track correctly. I use 3mm diameter x 2mm thick discs, but the 1mm thick discs might be more suitable for tiny objects. The diameter of 3mm makes it very easy to get the required 3mm spacing - you can use smaller magnets, but then have to get that bit right yourself. Possible future applications I have in mind are adding a pair of jousting knights to a medieval fair scene in front of New Sarum castle, and a small working canal boat layout. With imagination, there's lots and lots of potential.
For a quick way of shrinking photos, since you seen to be using Windows, you could just try good old MS Paint. Edit a picture file, select Image/Stretch-Skew and set both horizontal and vertical to 50% (or whatever), then save the file.