Usually you know where you are having problems, so you can set a breakpoint in your javascript code by placing the keyword "debugger;" on a line in your javascript code (obviously without the quotes) to set a breakpoint.
When you get to it in IE, it will ask you if you want to debug and prompt you to choose a debugger from a list, hopefully you will see Visual Studio in that list (both a new instance as well as your currently-running instance) - if you are using FireFox with FireBug, it will automatically stop execution on that line and you will be within the FireBug debugger, not Visual Studio.
You will want to do the following to setup IE for doing this - from within IE, follow this menu path: Tools > Internet Options > Advanced Tab > Uncheck the "Disable Script Debugging" options.