You don't have to decide on controller right now unless you have a strict budget. There WILL BE a controller for 400-600W that you are planning.
Can I put 4 x 100w instead of these massive 66"x39" 285w panels? I know I'm loosing 85w and it'll be more expensive but I really don't know where I would fit another one of these.
I meant one 285W on the side like you said, and "another" one on the rear part of the roof.
4*100 you can do either all parallel, or in pairs, or all-series.
5*100 you would have to wire all-series.
I would stay away from those flexible sheets. Solar Blvd had some square-shaped 80W rigid panels. When raised 3" above the roof (1.5" panel thickness, 1.5" from frame to roof), rigid panel won't disturb the balance or air turbulence on the road.