Shane,
I don't have an answer on what will actually happen to the views, etc. when you upgrade, sorry.
Regarding Client Configuration Templates vs. Client Templates...two totally different things.
Client Configuration Templates designate which views a user is
allowed to see, and can be used to lock down the
settings in client views, but they cannot be used to specify the
layout of the views.
Client Templates are, as you mention, "apply once" (either by the user accepting the template via popup message, or at next login) but they have
no capability to "lock down" the arrangement of the views or what the user is allowed to see/do with those views. Nothing at all to do with the settings. Also, if you apply the Client Template to a Workgroup, for example, then it only gets applied to
current members of the workgroup. When you add other users to the workgroup later, they
do not have that Client Template applied...you have to specifically apply it to the new people (and
not re-apply it to the whole workgroup unless you want everyone to get the notification that there is a new template to apply, and thus wipe out any changes they have made).
Kind of confusing, I know.