On the first point - yes. This is correct. The WA Framework strips away the design from the content as such. What you will find now is that you make a change to your template (either in design or code) you will only have to upload the template and all the files that are part of the theme attached to the template will pick up the changes - if that makes sense?
I've not actually comes across the issue in point 2 but it does sound like something is going amiss so hopefully WA will be able to get back to you on that one.