I have a lot of rules in my Mail.app but when my computer is off my inbox fills up with junk and it's hard to read from the phone. I want to set up the rules on iCloud but don't see a way of uploading/importing them into iCloud. Am I missing something or do I need to set them up again manually?
Try this. Go to iCloud.com and log in.
On the bottom left of the window, there is a cog:
Select that, and then Rules:
Finally, a window opens, and you can choose to sync Rules, or add specific rules just for iCloud.com (I think that's right.. not totally sure).
The help page is also useful.