Hey,
Ok so first, yeah, you're mirroring inside a layer, and both L_leg and R_leg will be in the same layer for a symmetrical model.
when mirroring first time, put character in bind pose, initialize mirror (in mirror tab), then you're ready to start mirroring as you paint (no need to go to bind pose anymore).
What happens to the "base weights" layer as you work on "legs" ? well, same as photoshop, nothing :) each layer has it's weights painted on a separate "plane", and behind the scenes, ngSkinTools interactivelly do a "flatten image" and write result into skinCluster. Only layer order matters, as weights on a upper layer overwrite whatever is painted on the lower layer. The key of why layers is awesome is that you can *remove* weights on the upper layer and it will uncover lower layer - something you cannot do without layers. Imagine in photoshop, you have a picture of Bahamas and a picture of you, and you want to make it look like you've spent your holidays there, you put Bahamas in background, yourself in foreground, and delete everything around your silhouette on the foreground; you further work with the silhouette, applying feather on the edge, adjusting color balance, but this does not affect Bahamas at all, you're not even worried that you'll screw up that picture, you only focus of blending in your face right. Some pixels around the edges of your face will not be 100% opaque, so they will be a blend of picture of you and a picture of Bahamas.
Also it's best of the picture of Bahamas does not include another face in the foreground.
Now imagine that
Bahamas = character torso;
Your face = character legs
You paint character torso weights on the lower layer and keep it there. You don't paint legs or anything else there, really, each layer, including base one, should have a purpose ("no another face in the Bahamas layer").
Then you start working on the legs, and you can just focus on getting the legs right - start with rough silhouette, experiment on adding and removing weights, inspect how it blends in - and you are never overwriting character torso weights, whatever you choose not be weighted to legs, will stay weighted to torso.
Does this clarify things a bit? :)