Do you need Velcro for a pedal board?
Velcro can be a viable alternative in some cases, but it is less sturdy and needs completely flat surfaces to work. For example, Velcro isn't thick enough to work with most wah-pedals, even if you've removed the rubber feet. Also large and heavy pedals can prove especially difficult to keep in place.
Which side of Velcro goes on pedal board?
In the end, it really doesn't matter which side it goes on, it's your stuff, you can do whatever you please with it. As long as your pedals aren't falling off the board then it's purpose has been served.