Map heights.tga
The map_heights.tga is the tga that controls both the coastline and the heights displayed on the campaign map.
Fig1. Reduced version of the vanilla RTR map_heights.tga
The blue areas represent the sea areas - these areas will be water in the campaign map regardless of any different areas marked as sea in map_regions.tga and map_ground_types.tga. If there is any discrepancy between these files the sea area shown in map_heights.tga is always used. The game applies a default ground or water type to any mismatched areas in map_ground_types and extends or contracts the regions shown in map_regions to fit. In RTW and BI (not M2TW) a corrected_regions.tga is generated and placed in the Rome - Total War folder each time a campaign is started, the corrected_regions.tga shows the adjustment the game has made to make the map_regions.tga fit the map_heights.
The blue colour normally used for the sea is RGB 0,0,253. Slight adjustments can be made to this colour, see here for discussion on adjusting the colour to get rid of triangular projections along coastlines.
Land areas are represented in grey scale pixels, eg: RGB values from 1,1,1, to 255,255,255. A true black of 0,0,0 is taken by the game to mean sea (and also produces odd flashing graphics) unless you are using a map_heights.hgt in which case 0,0,0 values seem to convert correctly.
For 'real world' based maps satellite data can be downloaded and used as basis for the map_heights.tga see How I Make my Maps by BDH. This gives a quick start towards the making of an accurate map, however much manual editing normally needs to done to the heights map afterwards to sort out coastlines and make sure that areas battles can be fought on are not ridiculously steep.