Never mind, I found the way. For future references, if you want to replace the musket sounds of NTW3 follow the steps bellow,
1. Download Pack File Manager here.
2. Unzip the Pack File Manager ZIP file.
3. From this link download General Andy's Musket Sounds (you will need to log-in to download).
4. Unzip onto your desktop.
5. Launch the application by clicking PackFileManager.exe
6. From the top menu select File ---> Open.
7. Open folders until you find the folders name sfx.
8. Select the file sfx.
9. From the top menu select Files ---> Extract ---> Extract Selected.
10. Put it onto your desktop.
11. Now, again from the top menu go to File ---> Open and look for the following path asuming you have the Steam version of the game,
C:\Program Files (x86)\Steam\SteamApps\common\Napoleon Total War\data\mod NTW3_hb_patch_v361.pack
12. Inside that pack file you will find a folder name sfx. Open sfx ---> weapons ---> muskets and you will find the files you have to replace with General Andy's Musket Sounds files.
13. Backup that sfx folder before proceeding to replace them by following step #9 in case something goes wrong.
14. Now, you will have to replace, one by one, the files on the folder musket. Don't worry, they have the same names, from the General Andy's Musket Sounds folder to the NTW3 folder.
15. Select the file you want to replace (e.g. emp_hyb_weapon_musketfire_01_v1.00_gme.wav) then go to Files ---> Replace File , look into the General Andy's Musket Sounds folder folder for the file with the same name.
16. Repeat #15 until all files have been replaced. DO NOT TOUCH, emp_hyb_weapon_musketfire_16_v1.00_gme.wav AND emp_hyb_weapon_musketfire_17_v1.00_gme.wav.
That's it, hope this will help people like me in the future.
Cheers...