Right now there is no control over the order the layers are printed in Create PDF.
The colors are controlled by the settings in Setup, Display Colors, so you may be able to get some improvement by changing colors there.
This has been requested on Mentor Ideas as Idea D2644:
If you would like to vote for it please click on this link and enter D2644 in the Search box.
I've also put an idea out there for similar color control. It is D6588.