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Extract the binary into the game folder and execute it. It behaves the same as RPG_RT with the exception, that RPG2k and RPG2k3 games are automatically detected, so one executable works for all games (as long as they are supported).
If you want to install the official (propietary) RTP of RPG Maker 2000 and 2003 you need to install WINE.
Once WINE is installed you can download the RTP files as follows:
This website is written in Japanese only. Scroll down to the bottom of these files and click over the long blue button to download the RTP files for each as follows:
LANG=ja_JP.UTF-8 wine RPG2000RTP.exe
LANG=ja_JP.UTF-8 wine RPG2003RTP.exe