The roof caps for those look like this
https://steamcommunity.com/sharedfiles/filedetails/?id=2923007400
On upper floors you can hide chimneys inside interior walls
https://steamcommunity.com/sharedfiles/filedetails/?id=2923016073
and build decorative/functional rooms between those interior walls used to hide the chimneys
https://steamcommunity.com/sharedfiles/filedetails/?id=2923016112
https://steamcommunity.com/sharedfiles/filedetails/?id=2923016151
You could build your wooden add on to your stone tower similar to the way that I build my 2nd floor balcony
https://steamcommunity.com/sharedfiles/filedetails/?id=2923006749

You can build just about anything you can conceive of. Just experiment around until you get something that looks good to you. I'm not even all that creative but I took a few ideas from homes and other places that I have been and just kind of hacked at it until I got something I was happy with.