Your layout size can be anything you want. Your Window size, if uploading it to the Scirra Arcade, cannot exceed 800 pixels wide.
As for a "recommended" window size, you need to figure out your target device. If it's a mobile game you may want to keep it smaller like, 800x480 or 400x240. If you are targeting PCs you may want to start with a common 16:9 resolution. I think 1280x1024 is the new most commonly used resolution.