There could be a lot of different things going on here and we really need some more info to be helpful
* How long did you cycle your tank for and what were your water parameters (ammonia, nitrite, nitrate) after cycling? How high did your ammonia and nitrite spike during the cycle?
* Once you finished cycling, how big of a water change did you do?
* What are your parameters (ammonia, nitrite, nitrate, salinity, temp) today?
When you post your parameters, it is helpful to give us actual numbers and also to let us know what type of testing kit you are using!
What method did you use to acclimate these fish?
A few other things that could be helpful to you:
Fish often take several days to settle in to a tank. Hiding in the rocks and not schooling together isn't necessarily a sign that something is wrong, it might just be that they are taking their time getting used to their new home
It is not unheard of to add 3 chromis as your first fish. While not ideal to add more than a single fish in the beginning, a clown pair or 3 chromis are acceptable exceptions to this rule, but you really have to watch your water parameters carefully. That said, schooling fish tend to do better in odd numbers (3,5,etc), though I don't really know if the number is the problem. Also, even though they are schooling fish, chromis also tend to fight amongst themselves until only the strongest survives. There may be some bullying going on and causing stress to the non-dominant fish of the group. Feeding twice a day can help reduce bullying but can also stress your newly set-up system in terms of promoting algae blooms and increasing your nitrates. If you do start feeding more frequently, check your parameters often.
Finally, there are several of us here (myself included) who have not had great luck with Chromis in the last few months. Not exactly sure why so many of us have lost chromis recently but it may have to do with where they are being collected from or collection methods that have been used. I also started with 3 chromis and 2 of mine developed some strange illness (that I still haven't been able to identify) and died (thankfully the third is thriving).
So, bottom line is that there could be a lot of different things going on with your chromis - knowing more about your cycling methods, parameters, and acclimation methods will help us narrow down the possibilities and give you better guidance!