Scott,
If it's like most other snippets that you'd be putting into Joomla, I would have the Flash detection code in the same area as you're putting the flash movie you'll be displaying.
So if the flash movie was in a content item, insert the detection script into the content item.
If it's a module you're placing on the page, put the code in as part of the module.
If the code needs to be in the <head> </head> of the page, you might need to investigate a different method, or check joomla.org about how to create a module position in the head of the template.
Patrick
