Oh Shirley, this is a common and annoying issue. The reason it works fine to pull paper from the lower tray when you clean is that that's where it looks for paper when cleaning.
But when printing a document or photo, it looks for an optional setting, and it's very likely you just need to find and change that setting, and then it'll work from then on. At least until you need to change the setting again.
Are you trying now to print a document, or a photo? Are you using Word, or Photoshop Elements, or a web browser, or what piece of software to do the printing?
Typically a program like Word will have more than one way of printing something, but you don't want the quick way of doing it. Word for example will have a Quick Print icon in the top toolbar. If you hit that, you get no chance to change the paper tray setting. If you click File > Print, you can set it from there to either pull paper from below, or from above.
Another way to go is to look for Canon's Printing Preferences or Printer Properties window, something like that. Where you find that varies. Word for example will give you a way to select that in the File > Print area. If you find that window, you also get a chance to select and save where you want the paper to come from. Post back if you're still stuck, but be more specific about what software you're using to print and whether you want to use plain paper, photo paper, etc.
