Those boxes at the top will disappear when the new theme is applied as they are no longer even needed. I assume without looking yet that the login areas will also change as the new theme will not be black. In fact there could be problems with the new theme but those we will be able to work with and customize. The theme we have been using is mainly here now to make sure the forum will work and the information is being properly inserted. As you say, so far smooth sailing, and that is good news. I wish I could say that on this end.
What you do in the dark will someday come to light.