Ah, yes! Wine doesn't handle file transfers. You may want to get something like Filezilla (if you don't like the built in CLI equivalents) or anything else that does SFTP or SCP via GUI and use that for file transfers. Winbox works OK in emulators (or NOT EMULATORS), but it is an app native to Windows.
I do sometimes wonder if Mikrotik would be better off not marketing to SOHO users at all. The product is advanced, and expects you to have networking and sometimes systems backgrounds. For many users that's a very good thing, but new users are very frustrated sometimes.
On the other hand, the official manual is at wiki.mikrotik.com and while you can't edit the official manual you can make an account and write an article in the user contribution section that outlines in more detail how to upgrade, explaining these concepts to a level where you feel a complete novice would be able to follow. That way you can contribute back to the community and give future users like you something to read and follow step by step. That is, for better or for worse (in my opinion for the better) a corner stone of the Mikrotik support model. If you're not into network gear it's hard to appreciate how powerful these routers are for their price. Part of the reason is that there's not 500 people writing manuals that need their salaries paid every month.
Specific answers require specific questions. When in doubt, post the output of "/ip address print detail", "/ip route print detail", "/interface print detail", "/ip firewall export", and an accurate network diagram.