Unfortunately, VS2013's hlsl vertex/pixel shader compiling is a one input to one output file thing only. I solved this via writing a batch file to run fxc.exe on my input files and then setting it to run it as a postbuild event in the project's settings (ie. writing my own shader build system). Here's a few lines of batch file code to compile a simple vertex shader.
%shadercompile% input_hlsl.hlsl /E"%entryfuncName%" /Fo"output.cso" /Tvs_4_0 /nologo
Then all you have to do for a "compile on modifying shader source code" feature is to create a file after the process, check if input files are modified later than that lock file, then compile if true.