You can use either aerial - I think the red taped one is the main though... but they are part of a diversity system, so both go back to an antenna and antenna amp, so should work just as well as each other.
The fuzzy object... is the internal cabin temp sensor, that is supposed to be mounted behind that grille, yes.
Android units and CD stacker... no, I don't think it is possible for them to be connected and work. Most of the android units have a couple of USB connectors (some even have a microSD card slot on the front too) which you can load up a lot more music than would fit on 6 CD's ;)
I pulled my CD stacker out when I put aftermarket head unit in and use the space as extra storage under the sub!
'06 4.2 Supercharged Black/Cream "Jess" -- Bought April 2021 (NZ)
'01 4.6 Vogue Black/Lightstone "Snog" -- Bought Jan 2012
'99 4.6 HSE Cobar Blue/Lightstone -- Sold March 2009
'95 4.6 HSE Epsom Green/Tan -- Traded June 2008