Dear Andrew,
That is a tricky one to answer. I use different alignment techniques for different components, but generally, alignment requires a lot of forward planning when drawing. When drawing inside Inventor I use a tool called 'Constraint' which provides many options for aligning components. It can be tricky tool to use, particularly when used with big assemblies.
The rotor assembly described in my previous post uses a lot of axially symmetric components, and so the alignment was fairly straight forward. I drew a 1/2 section of the assembly in AutoCAD, imported the file into Sketchup (with the centreline), aligned the centreline of the 1/2 section with the blue axis, drew a circle on the red-green plane and centred on the origin and then used the 'follow me' tool to create the 3D shapes. Adopting this approach ensures that all components are correctly aligned.
The frame was drawn drawn inside Sketchup using different techniques. I used construction lines to mark out the positions of the support feet and then built the frame from the ground up, so to speak. I used construction lines to create alignment features on the support feet so that I could position the box sections etc.
When drawing 'inside' Sketchup I first create the component and open it to edit it. I then add alignment features which 'travel' with the component when it is closed (end edit) and moved. For example, suppose I want to align a bolt with a hole. When drawing the components I add centrelines to both the bolt and the hole so that I can use the ends of the centrelines for alignment. In the case of the bolt one would draw the centreline as long as the bolt's shank + threaded section so that the bolt snaps to the hole with the bolt's face against the mating part.
I also use TIG's AddVertex+.rb to add alignment points within the component (inside edit). The construction points then travel with the component when it is moved. What you have to avoid doing is using Delete Guides as this will delete the alignment points created by AddVertex+.rb.
Hope this helps,
Bob