You put these three tokens on other players' Locations with Open Production to produce the resources. It's one of your possible actions. In a turn you can send your workers to three such locations at most. Each time you do it you give the owner a worker and put your token on the Location to mark you've already been there this turn. You can't go to the same Location twice.
I guess by base tokens you mean the tokens in the colour of you faction.
One of those is used to mark your advance on the victory points track (we never use that), I guess that is the one you already figured out. (You know, it is easier to answer questions if they are a bit less vague)
The other three are used to mark the open production facilities of other players you visited this turn, so you don't lose track: You are only allowed to visit each open production of your opponents once per turn, and only three in total. Don't forget to pay your opponent 1 worker for the use of his production.