I defined alignments and a surface in Civil 3d, then reopened the same drawing in Autocad 2012 to amend some line work (just because I like drafting in this better). When I next needed to do an inquiry off the surface, I opened the drawing in C3D, but all the alignments and my surfaces were gone! Why doesn't C3D retain alignments/surfaces after you've opened a drawing in Autocad 2012? Would you recommend keeping a separate C3D base drawing for the design work, and another for the drafting? and just xref-ing between the two? Any advice you can provide is appreciated. Thank you!
For the future, do you know about the "Autocad Civil 3D as Autocad 2012" launch option? (it's on the Windows Start menu). This give you the plain ACad interface for plain drafting (but you are using C3D) without having to worry about plain Autocad messing up your C3D files (as it appears happened to you).
In addition to what Mike said, there are also workspaces that give you the "autocad" interface you may be seeking. Try switching your workspace to the 2D Drafting & Annotation and see if that doesn't give you what you want. To answer your 2d question, yes. We keep all our data as separate as possible. BaseModel.dwg for existing conditions. EG Surface.dwg for the topo surface. Roadway.dwg for alignments & profiles (we only do transportation). Creating data references of all of those to use in the Corridor.dwg and any other dwgs.
HTH