The theory from these links show that the order of Convolutional Network is: Convolutional Layer - Non-linear Activation - Pooling Layer.
Well, max-pooling and monotonely increasing non-linearities commute. This means that MaxPool(Relu(x)) = Relu(MaxPool(x)) for any input. So the result is the same in that case. So it is technically better to first subsample through max-pooling and then apply the non-linearity (if it is costly, such as the sigmoid). In practice it is often done the other way round - it doesn't seem to change much in performance.
As for conv2D, it does not flip the kernel. It implements exactly the definition of convolution. This is a linear operation, so you have to add the non-linearity yourself in the next step, e.g. theano.tensor.nnet.relu.