layer>new adjustment layers>color balance, if you do ctrl+b while your on a layer i believe it will only color that one layer instead of all of em
sounds to me that your using a color balance as in Image -> Adjustments -> color balance if this is correct, what your gonna want to do is go to: layer -> new adjustment layer -> color balance and move that to the top hope that helps
if you are done with it, go to image+apply image+colorbalance...but if you arent go to layer+new adjustment layer+color balance.