WinSCP synchronization.

Does going to Commands > Synchronize, and synchronize with a folder in my computer make it so that the FTP im connected to gets the same files as the folder in my computer, or other way around, the folder in my computer gets the same files as the files in the FTP? I'm a bit confused and don't want to mess anything up.

It depends on the direction you select:
https://winscp.net/eng/docs/ui_synchronize

Ahh okay, so if I click Local it will compare the remote files to the local, and then copy any files the local folder is missing over?

Yes. It also copies updated files, not only missing files (with all other settings being default).