My first thought was to simply take a saucer, fuse a fuselage, and then attach nacelles using wings for pylons.
I know that it can't be that simple.
A major consideration is just how advanced the engineering is.
Are they advanced enough to the point that aesthetics can come before function, and thus the ships are as much a form of art as they serve a purpose?
Or is the technology still primitive enough to a point where form follows function, and thus aesthetics is the last thing thought of during the design process?
I think that the differences in shape between, say the vessels depicted in Star Trek and Babylon 5, I cannot help but think illustrates this in a microcosm form, and not just because they are from completely different television series, but also because of technology. Earth Alliance in Babylon 5 namely lacks shield and artificial gravity technology, which the Federation has, even though the two series exists in the relatively same time period.
The differences between the Constitution class, and the more sculpt-like Galaxy class further illustrates the part that technology plays in determining how a ship will look.
Seeing as how the prevalent current theory seems to indicate that warp propulsion would use ring shaped unit(s), my current idea is using that, attached to a fuselage via a pair of wings, or even by an additional dorsal and ventral set of tail fins. The command hull would still be saucer shaped, fused directly to the fuselage, due to how great a shape it seems aesthetically, aerodynamically, and space-wise.
A triangular or an oval shape, or deviations thereof, could also work aesthetically as a command hull.
A more primitive technology might use a sphere shaped command hull instead, due to having even more room in it's influence, and being an efficient shape pressure-wise.
The sublight forms of propulsion could be placed on/in the command hull, or in the wings and fins (or both).
Another consideration to take into account is how volatile the power source is, and whether or not the forms of propulsion are hazardous, and if so, how much.
Will the power source and/or warp drive need to be easy separate from the inhabited parts of the ship?
This might determine how much the sections of the ship are all fused and integrated with one another.
This might also determine where most of the living quarters on the ship are.
Our understanding of how a warp drive might work could shape the look of the inside of the propulsion unit. For example, the Casimir Effect might be an essential part of the mechanism, which theorizes enough negative energy needed to warp space could be done by using two parallel plates.
If I understand the theory, the idea would be to place a pair of plates nano-meters apart, and then rotate the two in opposite directions, really fast like. This gives me the idea of these plates being rings instead: one outer, larger ring, and one smaller, inner ring, rotating in opposite directions at very high speeds. This would create the warp field.