I agree that the test templates generated by TestDirector are very "messy". The real benefit to these generated templates comes when you are not very familiar with the application. Having the test steps listed in the script, however, keep you from having to constantly refer back to the test steps.
You can use the template as a guide, but I would definately recommend removing the generated comments as you go and replace them with your own.
A compiled module doesn't actually test anything, so there is no reason for it to have test steps or to have an association to either a requirement or a defect. Most of the documenation provided by TestDirector involves test coverage and execution, so there is little benefit to having your compiled modules in TestDirector. I still suggest storing compiled modules in TestDirector so that your code is in one place with your other tests, but I would create a special subject folder specifically for compiled modules. Storing compiled modules in the same folder as other test can be confusing.
Further to the comments made above about the test templates generated by TestDirector being 'messy', I have a question: Does anybody know if it is possible to adjust what TestDirector provides by way of a script when the 'Generate Script' button is pressed? I presume that TestDirector somewhere has a definition of what to provide as a template script to the user, so I am asking if anyone knows where this definition is and if it can be altered?