http://www.linuxquestions.org/questi...h-wine-860048/
This might help with ADE not detecting your Kobo.
With installing ADE in Wine all I can do is post a few discussions.
http://ubuntuforums.org/showthread.php?t=701191
https://www.mobileread.com/forums/showthread.php?t=87518
http://appdb.winehq.org/objectManage...sion&iId=15545
Check the last link I gave to winehq as there are some good tips submitted by people towards the bottom of the page. Unfortunately as I dont use Wine (I use crossover office, a butchered version of Wine) I can't be more specific in helping you get ADE install.
Alternatively if you do a quick search here in the Kobo forum you can find a link to the Kobo Desktop app for Linux, which has a download link for Ubuntu, so that will allow you to buy ebooks from Kobo and sync them with your reader.