Here is what I do
1) Open SQL Profiler
2) Determine the counters that you need
**In my case I usually start with a blank template and add what I need to look at. If you are looking for query issues watch T-SQL: Statement
Completed and Stored Procedures: SP Completed. I use these because they both will show the full statement that is executed.
3) I set the Column filters so that I only see the Database I want to watch for performance by limiting it to a specific database ID
SELECT DBID FROM SYS.SYSDATABASES WHERE NAME = '
4) I set the column filters to watch for long running SQL Statements. This is done by setting the Duration setting to greater than or equal to 500
milliseconds. This may or may not be long enough for your Database, but the idea is to limit the number of returns that you see.
This will at least provide you a picture of what is going on in the Database. After that, you'll need to look at physical Server performance like disk queuing and memory swapping. However, that is OS level type stuff that indicates different issues.