Yes, it's okay. In fact some aquarists say you should let it sit and, as they say, "mature".
When I let mine sit too long I make sure to stir it back up a bit before I put it into the tank, salt tends to drop over time making the water in the bottom of the container have higher salinity than the water on top. If you are pouring the entire container in, then no big deal, but if you have a larger container, it might be.