To make sure that all the images in your PDF Templates display (and print) clearly it is best to save the file using the below settings:

DPI (Dots per Inch):    300dpi
Image Format:             .jpeg or .png
Colour Format:             RGB

*When using these settings it can adjust the height and width of your images to scale upwards. This is due to you increasing its resolution. To have this still display as the correct size on your PDF Template make sure that when importing the image remember to set the image size to the needed dimensions under "image properties".

Important:
This is for when placing images into your PDF and not related to the $my_cy_logo merge field.
This is also not relevant for email templates as the resizing feature will not work and the default resolution should be 72 dpi for anything other than print.