If you do this from within the game, your account should automatically be linked.
However if you already have a factorio.com account, you can link on the website:
https://www.factorio.com/settings
If you have linked your account, and are having problems, if you cannot register your account, if your account says not recognized or says email not found, please email into support[at]factorio.com with:
- Your factorio username
- Email address used to register
- Steam id
- Any other information you think might be useful