I would think if you want smaller files it would be best to shoot them small and not risk creating funky artifacts by downsizing. I suggest you set up a test. Mount the camera on a tripod and set up a shot like you usually take. Take the images both ways, downsize the larger ones and compare. The type of lens may even play into the mix.
BTW: I have the same camera and I love it. I shoot RAW-L and upload them that way unless the image is slightly soft.