I tried changing the slot in the palette originally but unfortunately they turned out not to be solid colours but different shades - too many to change each slot individually.
I'll relate the painful process I knocked up by trial and error just in case you guys have any tips for me. Maybe I should have asked before I started
Step 1 Index map icon: Using GIMP, open the map icon that has the background colour I want - lets call this the template. Index the image to generate a palette. Save the image under a new name.
Step 2 Open the template icon in a program called Irfan View (this is the main program I use to browse pcxs on my computer because it's really fast loading and neat). Use Irfan View to Export the palette as a PAL file (couldn't work out how to export/import palettes in GIMP).
Step 3 Open the map icon that needs a colour change and repeat step 1.
Step 4 Open the map icon in Irfan View and Import the template's palette file.
Step 5 Open the map icon in GIMP and adjust the colours if necessary. Most times the palette was applied oddly and the wrong slots were being used. I had to use the paint pot to fill in the correct colour or use the pen to paint in individual pixels of the correct colour.
Step 6 Use GIMP to turn the image into a civ compatible pcx file and paste onto the resources.pcx sheet. I should point out that at this point the image had lost it's original transparency after saving it in Step 3. I had to then pen in magenta on the resource.pcx around the image where the transparency was now a white block of colour.
Move on to next image and repeat