You probably want to change a few things. In your (custom) CSS, you want to change both background-colors like:
.navbar-default {
background-color: #000000;
}
for the header and
#footer {
background-color: #FF0000;
}
for the footer.
Now, you will notice that those colors get overwritten by the .container
background-color. So, if you didn't change default IDs and classes, you probably want to override this with something like:
div.navbar-default > div.container {background-color:#000000;}
for the header and
div#footer > div.container {background-color:#FF0000;}
for the footer. As usual with CSS, make sure those styles get loaded in the correct order (that is, after the 'default' bootstrap CSS file has been loaded). Good luck.