SpartanUI doesn't use a WTF folder, as the UI is hardcoded to look that way (besides Bartender, where SpartanUI hooks into the Bartender code to set it up). If you try to change the bartender bars in spartanui, the next time you log in, they will be back the same as they were on install - hence, hard-coded.
MazzleUI uses a combination of a WTF folder that needs copied over and hooking into addon code to set things up.
Anyway, the addon cannot copy settings from your folder. Best thing is to include all saved variables and use default profiles when possible (or class profiles if it's different per class). If you must use some sort of profile selection or some such, then you will need to use that addon's api for selecting profiles, modifying things, etc.
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"You'd be surprised how many people violate this simple principle every day of their lives and try to fit square pegs into round holes, ignoring the clear reality that Things Are As They Are." -Benjamin Hoff, The Tao of Pooh
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