I'm working with Blender and I don't know how Blender units correspond to inches or cm. Is size something I'll define during the upload process here or is it something that I need to have somehow built into my model?
I use Sketchup instead of Blender. However, I imagine Blender might be able to export STL? If so, then you can use NetFabb to scale your STL to the right dimensions. Later, when you upload your STL to Shapeways, you can specify units (e.g., mm or inches). If Blender can't export STL, then you might need to export a format that Meshlab can change into STL. For example, Sketchup doesn't export STL, but it exports DAE, which I convert to STL using Meshlab. It's a quirky hodge-podge of tools to upload a 3D model, but, compared to the time to make the model itself, it's not a hassle.
A blender unit is subdivided into 10 units, which is good for metric sizes. There seems to be no problem using mm when you export to STL, as long as you consider a BU a 1mmx1mm sized area, and remember to rotate the model where its Y axis is aligned to the Z global axis.