This did not answer my question. When you said that "the photos stored on your Mac would be uploaded again when you enable iCloud Photos", I took that to mean I need to delete my photos before I connect so I don't have duplicates in my iCloud.
I deleted all of the photos off my computer, then reconnected to iCloud. Well... as soon as I reconnected to the cloud, iCloud took my delete photos command on my local hard drive to mean to delete all of my photos. After I realized this I went through my recently deleted photos on my computer and selected the ones to save. It seems like iCloud is now following my computer as it deleted all the photos and is now restoring the ones I selected. My phone went through the same delayed process.
Seeing as my computer is still glitching and I will probably have to send it off again, does anyone have an answer to this? Without an answer I plan on just reconnecting to iCloud (without deleting my photos off the local drive) and cross my fingers that it doesn't duplicate all of the photos already on my computer.