Exactly. That so why I ask. How can I know what side I should solder them ? Numbers on the silkscreen ? Assuming the left leg of my pot (withat shaft up) Is the number 1 ?
By the way. Nice board. I dream of designing a clean looking board with everything on board like that. But I'm so afraid to mess up the dimensions that I never dare doing it. What is the plug in the top for? Power? Where do you buy those plugs? How about the long legs pots? Where can you buy those? Are these specific jacks? Low profile or normal ones? Also, do you need to avoid putting some components under the pots? Like electrolytic caps or idk. How do you solder the smd ics? And most important question ... What is it? 
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The board isn't mine, is a FV-1 board from Ice-9 @DIYstompboxes. You can get one in oshpark

The plug in the top is for EEPROM programming I think.
Regarding SMD soldering, there are a lot of techniques and lot of questions have been answered here in the forum. For me the essential thing is a good pair of tweezers and lots of flux, but try searching smt or smd soldering here, you'll find lots of info.
About how to know how to solder pots: most of the time, you have to solder them on the down side, like on Juansolo's Dipthonizer but, as you said, silkscreen is a good clue.
If you take a look at madbean's standar wiring diagram (I recommend you to print it and have it on your desk, at least at the beggining) you could see how it goes:
http://www.madbeanpedals.com/tutorials/downloads/StandardWiring_MBP.pdf1 is the left lug with your shaft up, and lugs facing down. Or right lug with shaft down.
As for designing layouts with everything on board, I find it a little unpractical (unless you're planning to make a really high run or get into production). It is really easy to mess it up .