<ol>
<li><p>If you pool twice with <code>stride=2</code> means you reduce by a factor 2 the image size twice, resulting with a total of x4 reduction (sub sampling) of image size. Hence, if you start with an image of size 256: 256/4=64.</p></li>
<li><p>How do choose kernel size, number of output of each layer, strides and other design parameters? There's actually no single answer for that and basically many papers/works approach the same tasks with different settings. AFAIK there's no clear guidelines or obvious choice of parameters that suits any specific task.<br>
That being said, you can find <a href="https://arxiv.org/abs/1611.00847" rel="nofollow noreferrer">this work</a> surveying some emerging deep nets design patterns.</p></li>
</ol>
How to design a CNN (the inputs and outputs of the layers)?
<p>I am a beginner and learning deep learning with baby steps. I have a question about designing the nets. I see in the papers, there are layers with different inputs/outputs and I do not know how to calculate/design before implementation. 
For instance, in this <a href="https://people.eecs.berkeley.edu/~jonlong/long_shelhamer_fcn.pdf" rel="nofollow noreferrer">paper</a>, there are some numbers beside the schematic layers output (see the following figure). How these filter size and other parameters are being specified for a network with a specific image size as input. 
<a href="https://people.eecs.berkeley.edu/~jonlong/long_shelhamer_fcn.pdf" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/V6L42.png" alt="enter image description here"></a></p>

<p>or in another paper, they have the following design:
<a href="https://i.stack.imgur.com/qFjQI.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/qFjQI.png" alt="enter image description here"></a></p>

<p>and they have mentioned, For a <code>256x256</code> input image,
the total sub-sampling factor of the network is <code>4</code>, resulting in
a <code>64x64xL array</code>, where L is the number of class labels. How this <code>64x64</code> size is being obtained?</p>

<p>How can I learn to design the net and calculates inputs/outputs of layers?</p>

<p>Thank you for any help</p>