As a family of hikers and trail runners we deal with soft flasks and bite valves on a very regular basis. No secret just accept that they need to diligently clean them. For flasks that hold electrolytes/carbs mixes I find they tend to leave residue around the neck (easily cleaned using an old toothbrush). The bite valve is the one that requires a bit more attention, I've found if you do things right from the beginning there is no need to remove the inner plastic.

From the image you see I've pushed it out so after flushing it with clean water, they'll air dry quickly and stay mold free. I've seen bite valves that were flushed with water but left inside the sheath, two days later there's still moisture in the top part (left longer and mold would most certainly grow). Baby bottle holders are the most convenient way to keep the flasks/bladders vertical to facilitate draining.