Maybe the problem's solution, which is most simple for the programmer and a user is to edit css via html form, maybe. I suppose, to create css-file, which would be "default" or "standart" for this application, and just to read it, for example, by perl script, edit in html and to write it down. Here is just the simple example.
In css-file we have string like:
border-color: #008a77;
we have to to read this string, split it up, and send to a file, which will write it down. Get something like this in Perl:
tr/ / /s;
($vari, $value) = split(/:/, _$);
# # While you read file, you can just at the time to put this into html form
echo($vari.":<input type = text name = ".$vari." value = ".$value.">");
And here it is, you've got just simple html-form-data, you just shoul overwrite your css-file with new data like this:
...
print $vari[i].": ".$value.";\n";
...
and voila - you've got programmatical way of changing css. Ofcourse, you have to make it more universal, and more close to your particular problem.