A brackish tank is a big step for a begginer, not only do you have all the problems associated with freshwater keeping but you also have the problem of keeping the specific gravity (salt content) stable.
A 10g is not big enough for the long term keeping of a green spotted puffer, when adult this fish will require a minimum of a 20g to be kept alone and a 40g if you want any hope of being able to keep tankmates with it, even then bigger would be better.
The others are correct in saying that transfering water will not help, water only contains bad bacteria and parasites (if they are present) and will not help in cycling the tank, the rocks may have contained some bacteria but they will have died within a few hours of being in the tank without a food source being supplied either by fish waste or ammonia being added.