This fragment confused me, because it looks like there are three substitutions. There aren't; there's only one. Read it as:
If you substitute fuel burning (which has subsonic propagation, and is used in every conventional engine) with fuel explosion (which has a supersonic wavefront)...
The first and third "with" link a noun (the respective process) with a property (how fast it shoots gas out the back). The second "with" is the substitution.
English is hard! I'm a native speaker, and I had to take a look at a few webpages to understand just this part! And I'm still left with questions, like why subsonic is described as having "propagation", but supersonic is described as having a "wavefront". Is this a distinction with a difference? I don't know.