A mortise and tenon is a great joint for many things, I find them to be very useful in furniture making, it all begins with layout, the tools I use for layout, are a square and a marking gauge, Shown here at the right is the marking gage being used to layout the tenon, please note that I shaded the layout lines and the areas to be removed with a pencil.

Here at left the marking gage is used to layout the mortise, the ends are marked with a square, I would like to note that, different mortise and tenon joints may require a different layout, these are flush, and not inset, so after choosing the face sides on both pieces, the settings on the gage remain constant, in other words....this time I was able to layout both the mortise and tenon at the same time, working from the face side strike all the left sides of the mortise and tenon, reset the gage to layout the right side of the joint and again, working from the same face side, repeat the layout. 

Personally I make the tenons first, using the table saw to rough out the tenon, I will cut the shoulders of the tenon first,  then nibble away the cheeks both of the cuts are made just shy of the layout lines, these will eventually all be fit one at a time to there respective mortise, also note that different depth settings will be needed for each cheek cut, since I thickness stock by hand, there may be small tiny inconsistencies ( and sometimes not so tiny ) in the stock thickness...if you always work from the face side, the "side that shows" will always be right, and the difference can be sanded or planed away on the other side...

The tools shown were used to take the tenons to there layout lines, work carefully to avoid going pasts the lines, and the tools from top to bottom are a simple chisel, a very old, but refurbished skewed rabbet plane ( also note the skewed rabbet plane is indispensable when working across the grain ) and finally a Lie-Nielsen low angle rabbeting block plane, used here like a shoulder plane...I am not sure if the photo shows it, but the tenons are now nicely  smooth and square...on now to the mortises...