When you use the line level in and out you are using the crossover and rolling your main speakers off at the subs crossover point.
On some equipment this can be a limitation yes. However, I think there are preamps out there that allow you to have control over each speaker individually so the sub can be crossed over or not and the speakers can be crossed over of not.
I'd look into the Anthem D1 or D2 if you want a high quality HT preamp with plenty of flexibility and that could also serve as a source for a decent two channel system or a two channel + sub system.