There is no sure fire step by step process to trouble shooting high CPU load on the SQL Server.
A first step would be to use SQL Profiler to see what queries are taking the longest, and the most CPU time. Open SQL Profiler from Start > Programs > Microsoft SQL Server 2005 > Performance Tools > SQL Server Profiler. Click the new Trace button (upper left) and connect to the SQL Server. The important events that you want to look at are the RPC:Completed and SQL:BatchCompleted. You will probably want to sent the filter to limit the data which is returned to you so that you don’t get all the commands which are coming back.
Once you have the commands which are taking the most CPU time you can run these commands in the Management Studio and see what the execution plan is. By reviewing the execution plan you can see what additional indexes need to be added to the database which will improve database performance and decrease the CPU load time.
When you start up SQL Profiler don’t run it on the Server’s console. Run it from a workstation and connect to the remote SQL Server. Running SQL Profiler on the servers console will make the problem worse as the SQL Profiler app requires a lot of memory and CPU to run.
Based on your description you may need to contact a local database consultant to have them look into your system. A good database consultant will be a bit pricy, but they can be worth every penny.