Hello Eugene,
The u-boot to be used depends on wether you will be using the FSP BSP Release or the FSL Community BSP. There is a bit more information on which layers are included on each on the following document:
YOCTO PROJECT LAYERS MIND MAP
The conf folder is located on the top of each layer, not every individual recipe, or you may use the conf folder on the Build directory for global changes.
I hope this helps!