Folder synch - starting afresh

eM looks great, but the first time I downloaded it I ticked the box to get it to get the info from Thunderbird, which I have on my PC but have never really used.  Subsequently, it seemed to copy everything over in one big Inbox folder, in a crazy order.  I tried uninstalling it and starting again, but by now it seemed set on just replicating its original appearance, and I couldn’t figure out how to get it to synch, instead, with my email server, Inbox.com.  Mailbird, which I tried later, flawlessly synched with that, re-creating the folders I’d set up on my server, but how can I get eM to do that?  It’s no use to me, otherwise.