If you want to mod graphics (or sounds), then it's basically a question of dropping the new files (.pcx format, for graphics) into the correct directory, over-writing or replacing the "Firaxis-original" files that are already there.
As always though, any time you're thinking about over-writing files or folders, first make sure you've made a backup copy of it/them!
For example, Civ3 Complete includes several user-created terrain-sets in the ...
[CivIII]/Conquests/Scenarios/ folder (I use
@Sn00py's).
These are 'art-only' mods, and the simplest way to use them is to go through the "Civ-Content" menu (which looks at the ...
/Scenarios/ folder). The game executable will then start a normal epic-game based on the otherwise unmodded Firaxis ruleset (.biq) file, but using the modded terrain, rather than the default Firaxis terrain. Since such a game will be played using the default rules, it will be counted as valid for inclusion on your own scoreboard, or possibly even submission to the Civfanatics Hall of Fame (provided it also meets all the other criteria for HoF-submission, anyway).
But to have those modded terrains show up in an epic-game started via the "New Game" menu-option, or in a Scenario which has no terrain-set of its own (and would therefore use the default Firaxis terrain) — such as one of the Firaxis Conquests — you would need to copy all the (terrain .pcx) files from the relevant terrain-mod Scenario's
..Art/Terrain/ folder, into your ...
[CivIII]/Conquests/Art/Terrain/ folder (making a backup of that folder first, e.g. ...
[CivIII]/Conquests/Art/Terrain ORIGINAL/, just in case!).
I also use
@Puppeteer's
'Popheads' graphics-mod, which adds small smiley-faces below the default Firaxis popheads. That file is located in ...
[CivIII]/Conquests/Art/Terrain/. You can
look at his thread about it, or he has made an excellent set of tutorial videos showing
how he installs Civ III, and also
how to include the modded pophead file.
Other graphics can be similarly modded, including leaderheads.