Rectangle Box Filling Unusual Result

[westdr1dw]

I have a wiring diagram which I am trying to fill boxes with color to facilitate reading. The boxes have labels and I am only trying to fill the box around the label. I have already filled 6-7 boxes exactly the way I wanted. However, came across one of the boxes where no matter what I did it placed a the rectangle box I created under the box on the sheet. Now I am getting two options. Preserve transparency or fill the box. I do not want either of these options. I want to fill the box retaining what is already on the drawing.
I am working from a PDF file opened using PS.

Any help is appreciated.

[Bojan Živković]

Can you please post screenshot with Layers panel visible?

[westdr1dw]

This is the second post as I have not seen the intial post appear.

I have a file in latest ver PS which is an Acrobat file. I have encountred a few issues. The image is of a wiring diagram for electrcial circuit.

1) 99% of the boxes are transparent. A couple of the boxes are filled with ? 

2) Started out being able to fill the transparent boxes with color using the rectangle box and fill. However did not realize the boxes were not transparent and using the above process would cover the area completely. I must have triggered something bc when I went to another transparent box I was not able to replicate previous step in rectangle/fill. However developed a workaround by selecting the box and creating a new layer. Once I filled the box on the original drawing with color, I could then copt and paste the newly created  layer over the color filled layer. 

3) The boxes with the filled (?) stated above cannot be converted to transparent where the white pixels are showing.