A project like this will always be complicated, but I wonder if you are not complicating it in the wrong way!
When an object has many parts, many of which are identical, the usual approach would be to construct it using sub-entities. So for your ship have the six main parts (Command module, spine, service module, cargo pod, landing pod and engine) as separate models each with a dedicated texture. The benefit of this is that instead of a big complicated mess you have six relatively small and straightforward objects to work with, which are joined together later. The landing pod and engine would just be used several times each. This would also mean that changes could be made quite easily - for example you could re-texture say the cargo pod without having to touch any other part of the model or textures. Or you could remodel (and retexture) just the spine later if you wanted to do a more detailed version as your skills improve.
As for the texturing, forget MSPaint. It's a childs toy, not a graphics tool! I use Gimp but it sounds like you have access to Photoshop which is as good as it gets. The UV maps you are producing don't sound quite right yet - I would expect to see the outline of the faces, normally white on a coloured background or vice versa, which can then be developed in the graphics software. The texture can be built up using layers to give you a finished result. Take a look at my
texturing tutorial for one way to do this. This tutorial could use updating but is still valid, and although it is using Gimp, the same principles and techniques would apply to photoshop, and even most of the tools will be similarly named I expect.