I use Boxcryptor on my iMac to backup to Google Drive. Before running the backup program I go to Google Drive preferences and select "pause" and once the backup is complete I select "resume." This helps with CPU management and seems to keep things in order (possibly, all in my head, but that's how I do it).
What I do notice is that unlike backing up to a local drive, there are times that backing up to the Boxcryptor/Google folder (even with Google Drive paused) seems to slow down quite a lot. I'm assuming that there's some process whereby Boxcryptor is intercepting the files prior to putting them into the Google Drive folder (hope I'm somewhat making myself clear).
If there was a way to have Boxcryptor "pause" whatever it is that it is doing in the background, it might be helpful.