1. The best solution for automating obfuscation is MSBuild integration offered by Spices.Obfuscator, please find NineRays.Build.Tasks.dll and documentation how to use tasks offered by that assembly.
Also you can use Spices.Obfuscator in your C#/VB.Net scripts - see the example project in \SDK\SimpleObfuscator.
To solve problem with AssemblyResolver that pop-ups each time when Spices.Obfuscator can't resolve reference to assembly, you should specify search paths (/PATHS argument) to provide Spices.Obfuscator with paths for automatic assembly resolution.
2. Yes, you can export obfuscation results to obfuscation map format (that obfuscation map you can open in Spices.Net environment). Unfortunately that option isn't supported by command line, but you can create Spices.Project file (with Spices.Net environment or OptionsGUI utility coming with Spices.Obfuscator console) and specify Spices.Project.ExportObfuscationMapFile property in Spices.Project and use that file for obfuscation with MSBuild or Spices.Obfuscator console.