Generally, these patches are done like this:

1) Run patcher
2) Start a new project (can be deleted later)
3) Close project
4) Take the RPG_RT.exe (Game.exe if it's RMXP) from that new project folder (it'll be patched) and copy/paste that over your old project's RPG_RT.exe (or Game.exe) to update it.
5) Enjoy new updated version

Of course, I have no idea which thing from which webiste and which version of RPG Maker we're talking about here, but that's the general process.