You can do two things:

• Save your folder pair as a location profile:
  https://winscp.net/eng/docs/task_navigate#bookmarks
  https://winscp.net/eng/docs/ui_locationprofile
  
• or "save" your synchronization task in a form of a desktop shortcut or a batch file, using a /synchronize command-line switch:
  https://winscp.net/eng/docs/commandline#synchronize
  

Nah, I think you got it.

I wanted to know, if I can save each sync as its own task or if I have to always choose the folders manually?

Sorry, I do not understand. So why don't select the specific parent folder for the synchronization?

As an example, I have 3 parent folders with several layers of sub-folders below. The layers are totaling about 500 folders. I only want WinSCP to sync one of the parent folders each time (3 tasks), not all 3 at once (1 task). Changes often are only made to one of the parent folders.

I hope, that clarifies your question.

Are those directories somehow related? I mean are they for example subfolders of the same parent folder (but there are other subfolders that you do not want to synchronize)? Or are those just random folders scattered around file system?

I tried to find more information in the documentation, but to no avail.

Is it possible to use file synchronization to assign tasks for multiple folders, that you can select which one should be synchronized? I have several rather large folders and I don't want, that WinSCP always needs to check the complete server for changes. FreeFileSync has the ability, but it doesn't work with WebDAV. The target server for synchronization doesn't support FTP.