I'm having trouble getting the results you are reporting. With version 2.0.6 using a SiteAssist template I first created the pages from this template, then in the DataAssist wizard I specified this template and the pages that I had already created. I did not get any warnings or errors doing this.
Once the pages were complete it seems that all of the DataAssist forms were entered into the correct editable region that I selected on page one of the wizard. Perhaps there is an issue with the template you are using, I'm not sure though. If you can please post back with the template you are working with and the steps you are taking to produce the pages and get the bad results. I will use your info to try and reproduce the problem so it can be looked into further.