To smoothen up the cockpit, I think you could make the brick structure around the cockpit piece a stud or two shorter, so that the front edges wouldn't stick out that badly. Then you could indeed use inverted slopes to make the bottom of the cockpit more round and, if you have enough slopes, also so long that it would reach the main body, thus giving the craft more solid look.
As for the troop bay, I think a major factor in the blocky look are the strictly rectangular apertures on the sides and the rear. Therefore, it might be enough if you just put some 1x2 slopes on the lower and upper corners of the holes. The studs on the slope bricks would still be visible, since the bricks couldn't be entirely integrated into the structure, but putting the round little 1x1 bricks on the studs - and perhaps onto the underside of the slope pieces in the upper corners, too - would solve the case.
Other than that, you could always just play around with slope pieces and try to stick them at places and see, whether it increases or decreases the blockyness.
Greebling the vessel more on the problem spots might also be an efficient way to make the craft less blocky. It may not be as smooth as sloping, but it would at least give some shape.
There are my ideas. I only hope you understand them, too; my English could most likely be quite a bit clearer.
EDIT: Speaking of the cockpit area, I just came across
this, a neat MOC by a fellow Bothan, Brick shock aka ODST7. It uses the same cockpit piece, so perhaps it'll give you some inspiration.
