Hand soldering SMD 1206 components
You will likely find that 1206 are actually quite easy to hand solder. When you get used to SMD boards, you will find they are actually quite large. 

With a standard iron, I find it quite simple to hand solder 0603 components, and with a small precision iron, 0402 can be done. 

Your best bet and my recommendation if you haven't don't it before is to pre-solder one of the pads, then heat up the solder with your iron, and place the component with tweezers. Once you are happy with the position, remove the iron then simply solder the other side. This is by far the best way if you aren't sure about your soldering skills.

If you have access to some flux, then make sure to use it!

If you want, you can make a PCB with a few different footprints on it, have a few 1206, a few 0805, some 0603 and so on, and use it as a 'practise board'. This way, you can develop your SMD soldering skills, and when you get more confident, you can switch to making PCBs with 0805 or 0603 components, as the larger sizes are getting harder to come by!

After @pipe pointed out the link in the question, I don't really have much to say on it. I have never ended up with a cracked capacitor or any component. The article seems to be talking about the heat shock of the component, and cracks occuring during the rapid heating and cooling of the component and the solder. By only soldering one side at a time, that should reduce these stresses anyway, the article seems to point to both sides being soldered very quickly, or at the same time. It also mentions that is can cause failures during a "board bending resistance test" which I assume is not needed in your application! So really, I wouldn't worry too much about it. If you do find on the off chance you have a broken capacitor, just replace it!