if I go to switch themes do I have to go to original first then install new theme or do the new themes just overtake the old one and work fine?
It will work fine. However if the old theme has something installed that the new one does not, you will have the old version of that apk remain.
Best bet would be to reinstall the vanilla version and install the new theme over it.
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Search "kookahdoo" on the market for my themed apps.