Since you pruchased from the website I'll assume that you bought it via Humble and not via Steam.
If you linked your purchase with a humble bundle account you can log in on their website and go to "My Library". There, just download the game again, it'll be the newest version.
If you haven't linked your purchase you need the link that was originally sent to you via email. That's where you downloaded the game the first time. Just download it again, that'll be the newest version. You might also want to link your purchase with a humble bundle account now, it will make updating easier in the future.
Either way, to keep your built machines and what levels you completed, copy the "Saved Machines" folder and the CompletedLevels.txt file from the old game folder to the new one.