Configuration of Yaesu VX-6, WinLink, and SoundModem

How can I improve the waterfall accuracy of the Sound Modem?

What parameter do you refer to as “accuracy”?
If it’s bandwidth you refer to, then you only get a few KHz by reading from radio’s audio output. You’ll need I/Q output to get a wider view into the band. If you mean resolution (bit depth) then it’s also likely bottlenecked by the radio. Digirig’s audio input is sampled at 16 bit which is more than enough for waterfall display. In software you typically have some adjustments for sensitivity and contrast of the data you visualizing.

After addressing everything you informed me about, the waterfall came through! Thanks.

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