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I have wordpress running multisite, on subdirectory there is installed Classipress.
The core is wordpress and classipress is only like a menu link.
I need these two instances to be equal in theme design, it means when browsing wordpress and all the posts the same design would be if clicked on ADS menu link. By clickling ADS menu link you are reconnected to www.mysite.com/ads/ and visitor sees the same design and layout.
Regarding which design should be used it is not a problem, I have configured Classipress alone with my own design, so same could be applied to wordpress, or I can choose some already created theme for wordpress and adapt it to classipress.