Chris, I think you may be on the limits of Solidworks to handle lots of parts or you have set a lot of relationships. I have ProE (WF2) and work in top down always. In ProE you can make an overall outline/shape skeleton assembly with just surfaces which you use to pik up geometry for othr parts but you need to be very careful with constraints and relationships. I set my planes up as a ground plane, a longitudinal plane through the centre of the car, and a transverse plane through the front wheels. Working from the skeleton I constrain all the parts and or sub assemblies relative to the x,y,z planes. I keep things like wheel hubs and uprights as a sub assembly. We have done cars, buses, trucks, earthmoving equip, food packaging machines etc in this manner. We try not to break parts up in sheetmetal but need to do so for large items to suit available material sizes and manufacturing machinery. Ie if you were doing the body of a car in freeform we construct it as a surface, cut it up into manageable sizes, apply an offset for thickness.
I do not know of Alibre software but suggest it would not have the capabilities of SW or ProE.
Hope this helps,
Trevor