The details vary a little bit depending on the state.

In my state, regular ballots go directly into the ballot box on election day and on early voting days. They get all mixed together so they are all counted.

The provisionals are in individual envelopes and in a separate container. The envelope identifies the provisional voter and the circumstances of why they were voting provisional. A few days after the election, the higher-ups evaluate the circumstances of each provisional voter to see whether or not the vote should count. This process is open to the public to attend and observe. A few disqualifiers include not being eligible to vote, voting in the wrong place, trying to vote more than once, etc. if the provisional voter is disqualified, the envelope is not opened and the ballot is not counted. If the voter is qualified to vote, then the envelope is opened and the ballot counted.

All ballots whether they be regular, provisional, or uncounted are stored in separate boxes for a few years in case there's ever a legal challenge to the election results.