I used to put the seats down and take my Cannondale apart, but it soon became apparent that this was going to damage the interior in the long run.
I bought myself a Thule system for about £150 all in - and Id recommend carrying the bike on the roof to anyone. On my old 1.2 it slowed the car up massively and even on my 16v I can feel it slowing, but it saves so much hassle and frees up the inside of the car for any luggage you might have.