You will need to do this programmatically, AFAIK.
Something along the lines of:
$(document).bind( "mobileinit", function () { ... $.mobile.page.prototype.options.contentTheme = "z";
Now, since there is no centralized connection, you will have to make a similar line for all theme parameters:
$.mobile.page.prototype.options.headerTheme $.mobile.page.prototype.options.footerTheme
etc.
I don't have a list of all of them, but a quick search for jquery.mobile-1.0rc1.js to search for .prototype.options. shows:
$.mobile.page.prototype.options.backBtnTheme $.mobile.page.prototype.options.headerTheme $.mobile.page.prototype.options.footerTheme $.mobile.page.prototype.options.contentTheme $.mobile.listview.prototype.options.filterTheme
it seems to me that you can go with them and find out more when you go. Note that not all of them are created like this: some of them are dynamically built in code. Find the Theme line to understand what I mean.
Update
$.mobile.page.prototype.options.theme should also be updated - based on Mokak's comment below.
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