In NT create a system environment variable (Start > Settings > Control Panel > System Icon > Environemt Tab...):
TNSADMIN and set it to whatever TNSNAMES.ORA file directory you want to use.

Variable: TNSADMIN
Value: oracle_home/network/admin (or the other one)

This will ensure that you are always using that particular TNSNAMES.ORA file in that dir.

The reason that you have multiple is that there are two instals of Oracle on that PC. You can also go to the Registery all the Oracle Installs under: HKEY_LOCAL_MACHINE > SOFTWARE > ORACLE

Good Luck.