well, let's see.
Q: "Should I only access Google Drive files from Boxcryptor going forward?"
A: Yes. To ensure that you have encrypted files, just work from now on only via the Boxcryptor drive.
Q: "If I access Google Drive from my browser, does it defeat the purpose of Boxcryptor?"
A: Yes. Working via a browser will lead to unencrypted files, there is no Boxcryptor.
Q: "Is it secure to work in Google Docs (from browser by default), or should I instead use MS Office (Word, Excel) and access/work from Boxcryptor?
Q: I've Boxcypt-encrypted my existing Google Drive folders, but by default it doesn't encrypt Google Docs, so now I have a duplicated unencrypted folder in Boxcryptor that has these unencrypted Gdoc "links"--should I simply delete these folders within Boxcryptor? Will my Gdocs remain on Google Drive?"
A: Google Docs/Sheets/etc. are NOT supported by Boxcryptor. These files contain only a link to the document which is only online, so Boxcryptor can't access it.
Here you must convert your Google documents to MS Office file and have "physical" files.
Q: "I'd like to share a Google Drive folder with clients securely. I understand Whisperly is to specific file sharing. It seems that I would share a folder directly from Google Drive. Clients then would access that shared folder from their Google Drive. So nowhere in this sharing process we are using Boxcryptor. How secure is this, and how can I make this process more secure, if possible?
A: With Whisply you can share encrypted files. Folders are shared file be file, that means, the receiver will get single files to download.
So, it's not a "real" sharing option in this case, as explained by you.