You can manually collect your by traveling to each and every mining location and clicking the gold bars and oakz floating over the miners. These pop up when there are oaks or some gold in the collection bags.
You can auto collect on all locations at once if auto collect is enabled on your account. To do this click on the locations/collect button the the bottom left of your screen
Then you can click the collect all button
Balances should update automatically if not refresh your browser.
For more assistance please watch this video