It's important to name things with the correct terms (which is quite difficult in Illustrator especially when coming from Photoshop). You probably don't want to add color to a layer, but to a path. You can also add it to alayer, but then all the paths on that layer would be the same color, which you probably do not want.
In order to color a path, select it using one of the selection arrows and then take the color panel r the swatches panel, select the stroke or the fill and mix the color.
Brushes get assigned via the brushes panel.
I actually want to set it so that each layer has a specific colour and path assigned to it, so when I flip between layers, I am also flipping between colours... I know I am not using the correct terminology... I am a student, and I use illustrator to mark up images. I am using each layer to mark a different series of structures in different colours, so it would help set the layers as a specific brush weight and colour... Hopefully, this semi-cleared up my question.
OK, then assigning everything to the layer would make sense.
So you need to target the layer by clicking on the circle to the right in the layers panel
Then in the appearance panel add a new stroke and assign a brush to it and color and whatever you need.
Other layer might need a fill. Process is the same.
There will always be at least one fill and one stroke when you add either.
Then you can draw on those layers and it would be best to have no appearance at all on the single paths.