I like to design bases based on what their purpose is.
For example, at the moment I am having a Voltz war with my cousin. I chose to keep my location hidden to prevent him from firng a dozen missiles at me as soon as the fighting begins like I plan on doing to him. Therefore, I needed a base that would have no minimap footprint and a hidden entrance. The most logical choice was an underground complex. It's nothing fancy, and the dirt and gravel patches are covered with just cobblestone, but it gets the job done.
The first room I dug was long and narrow with the ladder down at the other end, ideal for an automated turret if the location of my ase is compromised. Under that, I have a small wheat farm and a big pit for growing trees. Below that I have my machine room with my generators and machines.
At this point it's anything but pretty, but I plan on digging a shaft down to bedrock from the original room with a spiral staircase around the edge. Any more rooms I need will be dug off from there.
My point is.... well, I don't really have a point. But if there is one thing you can take away from this it woud be to start small, and don't be afraid to rip out huge sections of what you have already done to move you along towards your goal.