The cobrador will at some point collect the fares. Usually he will say “pasajes, pasajes” and make some sounds with the coins in his hand. This is the signal to pay your fare.
The best thing to do is pay S./ 1.00 and see what happens. Sometimes they give you the boleto (ticket) straight away. Sometimes they ask where you are going. Other times they say “sol veinte”, meaning you have to pay S./ 0.20 more.
If you are going for a short distance (8 blocks or so), try to get away with paying a china (S./ 0.50) if you can. Warning: this is not easy the first time!