What colour(s) do you need to change?
There are usually only three files you need to edit to make any style changes in PunBB 1.2x. Eg if you are using the default Oxygen theme:
YOURPUNFORUM/style/Oxygen.css
YOURPUNFORUM/style/imports/Oxygen_cs.css
YOURPUNFORUM/style/imports/base.css
A lot of the colour settings are in Oxygen_cs.css. Open it up and find the setting you are interested in changing and edit it. Use a CSS editor if necessary to open up and edit the file - eg TopStyle Lite.
If you aren't sure which bit of CSS needs editing, view the HTML source of the PunBB page you are interested in changing, and find out what CSS DIV or code is responsible for the section whose colour you want to change, then look it up in those three CSS files and change the colour there.
Even though it is a bit old, something like this
http://www.punres.org/desc.php?pid=39
will also help you visualize and understand which style does what in PunBB.
For more advanced style issues, searching this forum for specific help or the punres.org site would be a good idea.