I noticed that even after installing PTW, I get my changed terrain graphics and the little smileys in the city screen that show the citizen's mood, so those files don't get overwritten.
Concerning the bic: PTW uses a bix file instead, so that is used when you play PTW, if you play plain Civ3, it should be using the old bic file instead. Whether it gets overwritten during install, I don't know.
However, when you play a scenario in PTW, it chooses whatever graphics are included in the scenario. For things, that aren't included, it defaults to the Civ3 graphics.
PTW save games are in a different folder, so nothing gets overwritten there. Not sure however, whether you could play civ3 saves games with PTW, but you can always start civ3 to finish your previous games.
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