RawwkMost survival servers have an Admin Shop or just a command that lets you sell your item.

How do you set your base prices of the items?

Are you asking the criteria to set the prices or how to actually change things prices?

It all depends on how easy you want the server to be & the server game type.
Always remember that things used to craft should have a correct price acording to its ingredients. Lots of servers have bug exploits in this.
For example, it takes 9 wheat to make a hay block so its price should be divided by 9 so se the price for wheat.

1 Hay block = 100$
1 wheat = 11.1 (11.2 just to make sure its not exploitable)

I set the prices quite expensive because of the unlimited stock and to avoid economy fluctuations.