It won’t let me select “My Cloud” in the resulting menu and I instead have to upload to a specific sub-folder each time.
The answer, is, unfortunately, no. Not anymore. It was a feature that was previously existent. You could sync your entire local drive with your entire cloud drive. That feature was removed in an update to the software. I submitted a ticket about this very issue because I was sure I must have been missing something. I was not. It is the case that the feature was removed. You might think, like I did, that you’ll just go ahead and sync folder-by-folder. Not fun, but not a huge deal. Then you’ll find out that, also with an update, Icedrive introduced a 15 sync limit for no good reason that I can ascertain. Also in an update. You may, like I have, consolidate all your stuff into 15 folders to accommodate their arbitrarily imposed limit. Then you may, like I have, discover that they have recently reduced the frequency at which you get to sync those folders. My advice: never update.
Good luck.
We’re currently working on all new mount + sync app - We will add this ability 
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Thanks fam. I just read your other post about the upcoming changes and it looks pretty noice 
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