I'd definitely advise encrypting files yourself before uploading them rather than using pClouds encryption.
Having multiple generations of backups on pCloud ensures that if something were to get corrupted on my computer (and I couldn't recover it from one of my three local backups) I shouldn't have corrupted at least some of the pCloud backups. Since there's facility I can use on my Linux machine to mount my pCloud storage as just another filesystem, this is particularly easy to do.
My own preference is to encrypt any files (apart from music, videos and photos) before uploading them myself (using a scripted backup that runs overnight and does it all for me automatically). You certainly don't want changes made at pCloud to be reflected on your computer. It sounds like you've set up some sort of "both way" synchronisation, which is definitely not a good idea from the sound of it. I can't say I know anything about the built-in backup functions as I don't use them, but it sounds like you probably shouldn't either.
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