Post-production workflow: VFX before color correction?
Any workflow that works for you is "correct".  I don't see any obvious problems with your proposed workflow, though I would think you would want to do sound after VFX so that it can be properly timed to the VFX.  Depending on the software you are using, you may not have to lock the shots but may actually be able to move directly in to working on the shots.

As far as low contrast and low saturation, I would personally disagree with shooting for low contrast/low saturation.  This limits the depth of your available color space too much.  Your camera has a limited number of colors it can describe, if you ignore a large portion of that color space, then you can't describe as many colors and the resolution of your color after boosting the saturation and contrast will be very greatly reduced.  That said, if you have issues with lacking detail in your shadows, exposing it up in to mid-tones can help since your format doesn't actually support using that portion of the dynamic range anyway, so you wouldn't be losing anything meaningful.  

The key is that you want to make strong use of the color space your camera can capture and encode that way you have the highest possible use of the color space as long as you are careful not to exceed the color space (color clipping needs to be avoided).  It is always easy to make colors more subdued and to lower contrast as this is moving from a high color resolution to a low one, but you can't move the other way because you don't have the detail to fill in.

What flat means is not necessarily low contrast or low saturation, but rather that the colors are not heavily tinted and that details are well represented within the usable portion of the color space.  They can be fairly vibrant, but they have a neutral response and gamma.  In other words, you want it to evenly capture detail across the DR, but you also want the DR to be fully utilized.  Think of flat as the way the curve looks in the Photoshop curves tool.  Flat would be a straight line rather than a curved one.  It can still have very strong contrast and saturation since the DR is being fully used.

For the third part, it really doesn't matter.  Either you mix to subdued colors and boost everything or you mix to vibrant colors and bring it down.  Either way, as long as it fits at some point, it will fit when you adjust the color grade of the entire frame if it fit well before.