This is a procedure I learned from accomplished illustrator Don Long. I learned it entirely hand-drawn, but for convenience I'll do it in Photoshop here. And just as a disclaimer, I don't do this often, so don't expect a masterpiece!
First, in order to make the perspective reasonable, the vanishing points need to be pretty far apart. I want my final image to be 800 x 600, so I'm going to set up my canvas at 5000 x 600 pixels. I paint a horizon line a little below the top of the frame. This will ensure an overhead vantage point. As long as the entire spaceship that I am designing remains below the horizon line, the station point will be above it. (The "station point" is the place where the viewer appears to be standing.) If I move the horizon lower, so that the ship breaks the horizon, the apparent vantage will be lower. If the horizon is near the bottom of the page, we'll be looking at the bottom of the ship.
Once the horizon's been established, I do a transform to make it about twice as wide as the canvas; the reason for that will become apparent soon. Then I make several copies of the line and rotate each of them a little bit to form a radial grid. Once I have enough density, I merge the lines and move them toward one edge of the canvas, then duplicate them and move the copy to the other edge. Now I have this:
The initial line has to be twice the width of the canvas so that the grid will extend all the way to the opposite edge of the working area. If you have enough density of lines, you'll get a nice perspective grid in the center of the canvas:
I've reduced the opacity so that the lines don't create too much visual interference as I draw. I have also adjusted the hue of each side so that I have red coming from one direction and blue from the other. I also decided that I wanted to see more of the front of the ship rather than its side, so I moved the left-hand half of the grid inward, so the vanishing point is just outside of the guideline that marks the edge of my working area.
Now, with the perspective established, it's time to get to work. The first thing to be done is to draw a 3d cube that will contain the ship:
Since this is just two-point perspective, the verticals remain vertical, and the horizontal lines follow the perspective grid. The next step is to establish a center line on the bottom of the box. This can be done by finding the center point of the bottom plane and the center point of the bottom front edge. To find the former, draw an "x" from corner to corner in the bottom plane. Where the lines meet is the center of the plane. To find the latter, draw another "x" from corner to corner on the front plane. Again, the point where the lines meet is the center of the plane. Drop a vertical line from that point to the bottom edge, and that will mark the center of the edge. Then it's a simple matter of drawing a line through both of the points:
This cross trick can be used to find the center of any rectangle I draw, no matter its orientation. I put the bounding box on one layer, the crosses on a second, and the center line itself on a third. This way, I can control which reference lines I want to see at any given time. Were I doing this on paper, I'd be using a roll of tracing vellum and layering the sheets.
Using the cross trick and vertical lines drawn up from the centerline, I can confidently place primitive volumes (cubes, cylinders, etc) in the space and construct my spaceship a bit at a time. I check the perspective grid frequently to be sure things are lining up, and I occasionally use the cross to verify that things that should be centered are. Here's where my sketch is thus far:
As you can see, I decided to go ahead and break the horizon line after all, not to mention the sides of my box. I thought the shape wasn't very interesting, so I added those big pods. The one in the back is misaligned, but I'll fix that in the next draft. That's all for this evening 'cause it's time for bed. I'll try to pick this up again tomorrow.