I am pretty sure the Westminster assembly in Larger Catechsim 109, did not have in mind addressing "how" we think, but of creating unlawful images in our minds. We have to control such imaginings per the seventh commandment, so with the second. Before an artisan makes an idol, he no doubt has imagined it in his mind first. I expect we have a harder time of it now because our minds have been so flooded with detailed images from books, TV, movies, etc.
If you're reading the gospels and think of a man walking on water, is that a violation of the 2nd commandment? Or is it more if you are thinking of Jesus in specific detail?
If it is the former, how can you read the gospels and think about what is happening? Thanks.