If your sky is white on the film, its either an exposure mis calc or the sky was just white when you shot it, its not clear whether you want to replace a sky that was never recorded, recover a sky that has detail recorded on the film or balance exposure either at the point of shooting or printing.
Maybe you could try using filters on your film rather than at the printing stage.
For instance, a red filter will render blue sky's very dark, perhaps even black but will have little effect on clouds.
Are you using the contrast filters whilst printing because they will lengthen exposure times.
Also, a small enlargement is a more intense light than a larger one, thus shortening exposure times..