How to fill in the empty boxes with color in PDF?

Explain more about what these boxes are and what you want to do.  For example, is this a form field for user entry? Is it a display of some kind? Will it be dynamic,  or interactive?

There's not a straightforward method using Acrobat. You could add a button and make its border color noting and background color to what you want, and place it where you want and adjust its size to fit the space. Then flatten the page to convert the button appearance to regular page contents.