Hi Jim,
If I have understood you correctly and if you are using the Pro version of C1, this should be simple:
Make one recipe for your large jpeg. The Root Folder under the File tab should be set as Output Location. In the Sub Folder field in that tab, type 'Large jpg' or whatever you wish your folder to be named. This Sub Folder name is specific to and is saved with the individual recipe.
Make a second recipe for your small jpeg. The Root Folder should be Output Location as above, then type 'Small jpg' or whatever in the Sub Folder field.
Put a checkmark next to each recipe and process the files, which will be sorted into the relevant folders which have been automatically created within the default Output folder.
Some confusion can occur if you have previously set an alternative Destination in the Output Location 'tool' (window) - you may need to reset the tool via the ellipsis in the top right corner if this is the case.
Hope that helps.
Malcolm