If I have a box made of lines
__
|_|

and only the actual lines are layers in photoshop

how do I fill the box using that selection

(do not tell me to just make a filled box because I need to know the method for something where you cant just do that)

If it were me I would make a new layer and apply image and then use the bucket tool on that layer.

Gah bucket tool. I am dumb, I forgot about one of original computer art tools GAH!!!

Also if you have used the pen tool to draw a box inside your image, you can right click and go to 'Make Selection' and then fill that box inside.