If you want to catch all queries of a middleware like Hibernate or Ibatis, the simplest way is to use SQL Server profiler or to create a trace with SQLTrace stored procedures (sp_trace_create, sp_trace_setevent). With SQL Profiler you can save traces directly to a table, with SQLTrace stored procedure who produces a trc file, you will have to insert them in your table with sql statements. they are lot of examples on the web, for example here SQL Profiler have an option to generate the SQLTrace SQL script once you have defined your trace (File/export)
The SQL Profiler is in the developper edition but not in the Express edition. SQLTrace stored procedures are in all editions (IIRC).
You can generate the trace script on your developper edition and run it on your express edition. You can also create a stored proc that create and start the trace on server startup.