Somewhere in this thread it says:

The auto-clicker works when all of your spaces are full of mines, and then it clicks the next one that comes along. You will always have all your spaces full, it only clicks the oldest mine when the 6th one comes along.

Wait until just before the next mine is ready - when it says "STORE 00:01:00"  Check the balance of your account - maybe .001111  Then when the store says 00:00:00 check your balance again - it will have increased by your production amount.

But I don't think it clicks your bonuses - those are bonuses for logging in and clicking, so if you don't login, you don't get bonuses.