I am running a Pioneer head unit that extends the antenna whenever it is turned on, meaning that even if I am just playing a cd I have to fly the mast.
How can I rewire, with a switch to manual operation of the antenna?

 

I ran a spst on/off switch in my setup just like you're talking about doing.

I hope I can explain this well enough, I cut the pink wire (this one's from the antenna) and ran it to one pin on the switch , and used a 3M suitcase passthrough connector (so I didn't have to cut it) on the yellow wire which is the 12v switched line and that let me attach an extra wire to the other pin of the switch.

now I can turn off and on the antenna with the toggle switch.
Keep in mind these are the stock wire colors, aftermarket uses diferent colors
dark blue for power antenna and red for 12v switched is typical.

 

Thanks for the help!

 

theres a blue wire hooked up to the back of your deck, cut it a just place a switch in circut, bam, instant antenna.