In terms of how turbulent flow scales down to the molecular level, Kolmogorov's work
http://en.wikipedia.org/wiki/Kolmogorov_microscales
might shed insight into reconciling your thoughts. In a nutshell:
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Turbulence causes the formation of eddies of many different length scales. Most of the kinetic energy of the turbulent motion is contained in the large scale structures. The energy "cascades" from these large scale structures to smaller scale structures by an inertial and essentially inviscid mechanism. This process continues, creating smaller and smaller structures which produces a hierarchy of eddies. Eventually this process creates structures that are small enough that molecular diffusion becomes important and viscous dissipation of energy finally takes place. The scale at which this happens is the Kolmogorov length scale.
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