here are some general considerations for stereo images
A. The images should be ~63mm apart with respect to a point which you consider to be neutral, i.e. neither lies in front or in the back of the “zero-plane”
B. The distance of the images also put restrictions on their size, which is something you need to consider. Usually it is 1 ½ columns in a journal, if I am not mistaken.
C. For labels I use a program like photoshop or canvas, just because one has a wider selection of fonts and they produce antialiased renderings. I usually attach labels to landmarks, with which they share the same depth. For example if you want to label residue 234 and have the residue drawn in stick, you could place both upper left corners of the labels on the CA position, group them and move them out of the way so as they do not interfere with the rest of the graphic. Using this trick ensures that the labels appear in the correct depth.