I am have tried using edge loops and subdivide faces. But both created a square face on the round saucer section, I think this might still be the option, I might just need to re-align the vertices to get flush again?
Hard to know what you mean without giving a “before” and “after” image, so you can point out the things you don’t think work.
If you want to maintain the shape and just add more faces, you can also do that by using the “subdivision Surface” modifier. The only thing is that you need to change from “Catmull-Clark” to “Simple” and then press “Apply” to actual add it to the mesh, so you can edit them in edit mode.
Also, if it’s the top you are talking about and that is made out of one face, you can perhaps recreate it, using either a sphere, which will divide it in to faces that don’t get squared or create a cylinder, but in that case change the “Cap Fill Type” to “Triangle Fan” instead of using the NGon. this will also prevent you from getting things square at the top.
Your fine tuning has made a small line in the lower part of the ship. My guess is that you have some duplicate vertices, so try to use “Remove Doubles” in Edit mode after you have selected everything and see if you get some removed that should not be there.
Object properties -> display: wire and draw all edges
How those show up depends on the background, viewmode and shading, contrast between wire color and the faces, and modifier visibility settings. 3D view properties -> display and shading panels could be useful to adjust those.
The wires are there to show the mesh structure. When dealing with subdivision surface issues, it’s the unmodified structure that is most useful, so could turn the subdivision surface modifier off.
In the screenshot I included, the cubes from left are:
subdivision result with all edges
subdivision result with optimal display on (original cage, subdivided)
That way the structure is readable, but if you have to show the other side, could make a linked duplicate (alt+d) and rotate it. If you want to show both subdivision result and the structure, could make more duplicates to show them side by side, or make another screenshot that shows the structure and then the surface. But usually don’t need that, screenshots are for explaining things and the .blend file you include contains the rest.