My crawl space has gravel in it (ranch built in the 90s). It appears that some of ground under the gravel has plastic down, but some areas may not. The plastic also does run up the foundation wall like most recommened. My question is, does anyone forsee a problem with laying the vapor barrier over top of the gravel, or do I need pull the gravel backto one side and lay the plastic down and recover?

The gravel is just holding the vapor barrier in place. Move the gravel back a bit, overlap the vinyl and respread the gravel.

Depending on how bad your humidity and/or energy problems are, I would research sealing your crawlspace. Its almost always better to close up and seal the vents and access door. Generally, you would want to ensure that your vinyl Vapor Barrier is well sealed with this approach, but I might not bother with this step depending on the variables. Ventilated crawlspaces in new construction is increasingly recognized as bad practice.