Same home, but different desktops - xfce and unity


I noticed that my client is usable at unity, but if I switch to xfce, the client is not configured.

I suppose, if I configure the client on xfce, but it shares the same home and cloud folder as unity, there will be syncing problems?

Can I config the client, that it is working on xfce and unity at the same config?

Thank you.