Regarding server-side trace, I recommend reading these pages, either right after reading the Books Online documentation, or perhaps even before.
1. SQL Server Performance Statistics Using a Server Side Trace
http://www.mssqltips.com/tip.asp?tip=1035
2. Automating Server Side Tracing in SQL Server
http://vyaskn.tripod.com/server_side_tracing_in_sql_server.htm
The author of link 2 above has posted there a set of stored procedures that makes starting, stopping, and filtering the traces more encapsulated, which might also help you refine your troubleshooting.
Also, you can try to get the free book Mastering SQL Server Profiler by Brad McGehee.
I'm still learning these tools, too, so I can sympathize -- new DBAs and other people new to SQL Server may wonder why the performance monitoring tools aren't more obvious. I don't really know the answer to that one, but I do know that they are powerful once you learn them, and through Google and books you can find many people who have shared helpful ways to get to know the tools better.
Best of luck.
- webrunner