Custom XNA HLSL Shader Effects

I am attempting to understand how to perform custom HLSL Shader effects and mix them into our existing code.

We are using the content library with FBX models, and so I think the models may already have the textures inside that we need for specular lighting, and hopefully vertex modifiers. Here is the basic effect, I though that I should keep doing this loop like this and work with this effect?

foreach (BasicEffect effect in mesh.Effects)
{

}

List of objects:
3D Model - contains meshes with basic effects?
Basic Effect - should we use this anymore?
HLSL Shader Effect - this is what we want to use. Can we also stack other effects on top of this?