I don't understand what you mean "how is the sound from the rear deck affected with subs playing in the trunk". You need to expand a bit more on your question?
p.n.
The low frequency coming from the sub in the trunk should not affect your mid and highs if it is properly image. If you think that the sound coming from your speaker is distorted then you might want to try centering the FADE and BALANCE. Adjust the volume level so that all your mids and highs are playing at same volume level. Once all your mids and highs are adjusted then add in your sub for the low frequency. You can adjust the low frequency to your liking and the type of music that you listen to. If you adjust the volume correctly to all your speaker the sub should not affect how your speaker sound, but rather compliment the music that it is accompanying. As for the form baffle that you will put on. All it does is deepen and enhance the bass of the speaker with the sound reflecting of them.
p.n.
Actually it can, but not to the point where you will notice anything significant. The foam baffel thing would probably help you in those times where the bass really hits and causes a lot of air movement. But even if you touch your front speakers, assuming that they are off and the subs are playing, they too are going to pick up some resonance. Like said, it will effect your speakers, though not to the point of real noticeable sound quality degradation.
Jeff
-------------
Panasonic CQ-DX701 MXE Head Unit
MB Quart QM218.16Q
3 JL Audio 12W6
Street Glow Lighting