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.
I tried Ninja Gaiden 3. It's a lame turd with some flashyness. Sigma 2 was pretty decent compared to 3 ( And sigma 2 wasn't even good ). Now they are trying to polish their turd by porting it to wii u (LOL) and calling it enhanced version. Pretty smart. Next is probably Resident Evil 6 black ups (Like Operation Gears of War). I can understand popular titles (Local and foreign), but asking for shovelware 3.55 fixes just seems wrong to me.
but now i still can't get Ghost Recon future soldier to work... i replace 100 patch ... installed the game ... installed pkg file (BLUS30521_TCGRFS_103_N0DRM-PATBAT_REPACK.pkg)... then deleted the BLUS30521 gamedata in hh0/game folder... start the game and installed again the gamedata and then replace fixed 102 in hh0/game... try to start game again and i got black screen... no matter how long i waited...
btw the 102 N0DRM patch dont have any pkg file in it... where did you guys get it... is it the same as the one i got?...
and one more thing do you guys play the game disc less or with it in it...
does this one for harry potter & the deathly hallows part 2 actually work as tried a fix before and just got a black screen can someone confirm this one works, as tried a few and also Leatherface8 tried to help when i gave him the files and still didn't work, is a copy of the original game disc that i have