To debug shaders PIX needs to be able to locate PDBs for the shaders. The HLSLSymbols XDK sample demonstrates how to save PDBs to disk and make them available to PIX.
Vertex shaders can be debugged through the VS Output entry under VS Shaders in the Resources view. Simply select a vertex of interest, right-click, and select Debug this vertex. This opens the new HLSL Source view that allows you to set break-points, single step through the shader code and so forth. Next to the HLSL Source view is the new Watch view that allows you to track values of shader variables. Keep in mind that the values are only available as long as the underlying shader registers are available. Vertex shaders cannot currently be debugged when geometry shaders, or hull and domain shaders are used.
Similar to vertex shaders, to debug pixel shaders select a render target from the Resources tab and right click on a pixel to get pixel history. This gives you a list of draws that modified the selected pixel. Right-click the desired draw and select Debug this pixel. Again, this opens the new HLSL Source and Watch views allowing you to debug the relevant shader for the pixel.
To debug a compute shader navigate to the CS Shaders section of the Resources tab. From here, right-click the HW CS running as CS entry and select Debug compute shader.