3dscapture.com

When you capture it says you have an option to capture the top, bottom or both. If you capture only one screen is it full screen like ready to upload or do I have to crop it.

If you capture the bottom screen, you shouldn't have a problem. The top screen should be fine, unless you're playing an original DS game, in which case you'll need to crop it. The dimensions match those of the two screens.

You can Capture only Top, only Bottom, or both, if you desire.
However, the resolutions will be kept on 400x240 (single screen) or 400x480 (both screens), just like the actual 3DS resolution.
But don't be afraid, it's terribly easy to scale even 400x240 to 1200x720, with minimal quality loss.