The most secure method is a paper ballot handed to the voter at the polling station. The voter then goes into the privacy booth, makes their selection(s), folds the ballot and places said ballot in the box. The boxes are opened only after the polls close, and the public is free to view the counting at any and all times.
Any other method of balloting is far too vulnerable to fraud.
Early voting should only be for those unable to attend for professional or military reasons, and those ballots should be kept at the courthouse and counted the same day as regular ballots, the same way.
Haven't folks gotten sick and tired of "lost and/or late" military votes?