You may cover the dish with foil for only 15-20 minutes and then remove the foil. Leaving it on longer may cause the cream in the ramekins to get watery rather than the correct texture of a nice pudding.  After they've cooled down, remove the ramekins from the baking dish, cover with plastic wrap and refrigerate for at least 3 hours or up to 2 days.

Summary:
Pour the custard into the caramel-bottomed ramekins, and fill the baking dish with water so that the bottom halves of the ramekins are under water. Bake until the custard is set, which should take around 20 to 45 minutes. Let the custards cool down in the water bath. After the custard has been refrigerated, run a knife around the edge of each ramekin and invert the custard onto a nice plate, making sure you get all of the caramel out. Served.