I'm a bit confused about the problems you are experiencing. I think it would be best to work out one issue at a time. In regards to SiteAssist are you currently getting output from the wizard that is incorrect? If so what is incorrect about what the wizard is producing for you. Also, if you can post back with a copy of your Templates folder I can take a look to see what problems I experience when using your files.
As for check in and check out ability to keep the site synced up I don't think this is a good idea. I have never had a good result when relying on DW's check in/check out functionality. In my experience it is always best to manually check in and check out your files rather than rely on DW.
