You'll have to use the API to update by ID. It's not that hard, but you'll need the help of a software developer. You can export a list including the Marketo ID, but you'll need the API to save back the updates.
In the REST API, you can use the Marketo ID to update records:
http://developers.marketo.com/documentation/rest/createupdate-leads/. Potentially you can also use the "Import Lead" functionality and specify the Marketo ID as the lookup field:
http://developers.marketo.com/documentation/rest/import-lead/ (please test this, as I haven't done this myself yet).
In the SOAP API, you can do the same:
http://developers.marketo.com/documentation/soap/syncmultipleleads/ , however you cannot use the importToList function, because that only uses the email address for matching.