You can check your version from the top right of the menu. Once a day the game will check online for an update and SHOULD notify you of it when you start. You then need to re-use your humble widget download link to grab the installer again.
A better patch system is planned for the future
If you have lost your emails from humble you can get your order resent from this link:
Its safe to just reinstall over your old version. With any luck save games are unaffected