Pruning lemon trees can be a fun task. For many a lemon tree is exotic and has the sense of mystery around it. But clarification is the key to any task. And the more you learn, the more you will enjoy because lemons are a really fun tree to have around.
The limbs that grow vertically will flower just like the other limbs but generally won't bear any fruit.
Just trim them to the desired length, I usually make the cut right above a leaf node, some people suggest cutting at a 45° angle with the cut facing up to promote branching. I usually prune about 1/4 inch above the node. You'll be able to see where it was pruned, no matter where you choose to cut. But the branches are small so it won't be that noticeable. Lemon trees love to be pruned, you'll notice lots of new leaf growth a month or so after pruning.
There's some in depth pruning information avaialbe for the different types of lemon trees so find the one that works for you.
Meyer lemons are grafted, rather than being grown from seed.
The bottom half is called the rootstock and the top is the scion. The rootstock is chosen for its hearty root structure, likely from an orange or some other variety of lemon, and the scion is a cutting from a Meyer lemon which is a really exceptional type of lemon.
You can try and angle it a little so that the tree is sitting a little more vertically if you want. Also, you'll want to prune off anything that grows below the graft line. Anything that grows below the graft line will not be a lemon baring.
There are so many ways to work with these remarkable trees, more than are within the scope of this text, so I really suggest looking for the information that is suitable for your area and your type of lemon tree.