GPU PerfStudio supports the D3DPerfMarkers. Instead of using the PIX begin and end tags, you can use the following two entrypoints:
D3DPERF_BeginEvent(D3DCOLOR col, LPCWSTR wszName)
PIX also supports these entrypoints, so you should be able to use both tools. The name that is supplied to the begin event is visible just above the draw call selector before the name the of the draw call. It is also used in a tree control in the API Trace, and can be used as a State Group in the Frame Profiler.
Please let me know if this does not provide the functionality you are looking for.