I wouldn't mess with disconnecting a fuse for the second pump. Just leave the fuse alone.
The Racetronix unit comes with 2 pigtails for under the hood - a "red" one for the "red" pump and a "blue" one for the "blue" pump. When the unit arrives, both of these pigtails have jumper wires in them. This will cause both pumps to run. The idea is to have one pump jumpered so that it is your primary pump, and the other pigtail run to a hobbs switch. The hobbs switch gets triggered at 15psi and activates the secondary pump. When boost drops below 15 psi, the hobbs deactivates and kills power to the secondary pump so that you're only running on one pump (until you get above 15psi boost).
In order to run the Racetronix unit on one pump, you just pull one of the jumper wires from the under-hood pigtail. Doesn't matter which one. If you like, you can even plug in the hobbs switch to the pigtail (so as to keep dirt & junk out of the wiring connector). Then, just don't connect a vacuum / boost source to the hobbs; if the hobbs never sees boost, it never activates the relay to the secondary pump.
I make it sound a lot more complicated than it really is. Racetronix makes it VERY simple, I promise.
I don't know how Red's DP works.