If you are using the "patched pkg" file, I believe it is for the BLES version, so it will install in the incorrect folder. This is why I used the official BLUS 1.01 update.
However, to your original question. You will want to replace the eboot in the GAME/BLUS31002 folder yes. NOT the GAMES/BLUS31002 folder.
Easiest way I can recommend is to get the official BLUS update. Install it. Overwrite official eboot with the "patched" eboot.