@Ratte
AFAIK both CGX/P96 use something similar to DPMS to make monitorswitchers switch the display... If both HSYNC/VSYNC are enabled in the RTG side then RTG is displayed, otherwise AGA will be. AFAIK CGX/P96 turn off HSYNC and/or VSYNC signals in the gfx card when amiga screens are being shown.
both Radeon/Voodoo should include a 26pin VESA connector just in case you need extra signals in order to leave cleaner the original signal.
I don't know much about electronics but shouldn't that work without software (taking in account how cgx/p96 already work)?
