Here's how I can break it down as simply as possible:
Step 1: Put patch.dat & patch.fat in the folder with Gibbed's tools which can be downloaded from: Svn.gib.me
Note: Currently the GUI tools in the OP are out-dated and they are not updated very often. Unless the author starts making more frequent updates I would recommend against using it.
(To that mod author: please don't take that as an insult as it's not meant to be).
Put it in your games bin folder or in a place away from games files like C:\FC3\bin\
Step 2: Drag patch.fat over Gibbed.Dunia2.Unpack.exe. This will create a folder called "patch_unpack
or open CMD and paste:
C:\FC3\bin\Gibbed.Dunia2.Unpack.exe "C:\Games\Far Cry 3\data_win32\patch.fat" C:\FC3\patch
Step 3: Go into patch_unpack/worlds/fc3_main/generated/ and copy the file entitylibrary.fcb and drop it in the folder of Gibbed's tools
Step 4: Drag entitylibrary.fcb over Gibbed.Dunia2.ConvertBinaryObject.exe. This will create a new folder called "entitylibrary_converted". Inside the WeaponProperties/FC3 folder within is where you can modify the gun attributes. They're fairly self explanatory.
As an example of making some modding changes:
For making the Famas full-auto, open up FAMAS.xml and go to the line that reads:
Change that value to 0 and it will become full-auto.
As for ammo capacity, currently it's not known where the max ammo capacity values for the various ammo pouch sizes are stored, but if you meant the magazine size you can change that with the line that reads:
Step 5: When you're done making your changes to any of the files in entitylibrary_converted look for a file that will have been created in the main tools directory called "entitylibrary_converted.xml". Drag this file over Gibbed.Dunia2.ConvertBinaryObject.exe to create entitylibrary_converted.fcb (rename this to entitylibrary.fcb. Now place it in patch_unpack/worlds/fc3_main/generated/ and overwrite the file that's already there.
Step 6: In the main tools directory drag the "patch_unpack" folder over Gibbed.Dunia2.Pack.exe. It will create two files: patch_unpack.dat & patch_unpack.fat. Rename these to patch.dat & patch.fat and put them in the data_win32 directory of your main Far Cry 3 game folder.
or open CMD and paste:
C:\FC3\bin\Gibbed.Dunia2.Pack.exe -c "C:\Games\Far Cry 3\data_win32\patch.fat" C:\FC3\patch
Hope that helped. That's just a common set of files to be modified, there's a bunch more than can be unpacked from common.fat/dat and fc3_main.fat/dat.
You'll encounter other files that get unpacked that take the form of .lib or .obj. You just drag these files over Gibbed.Dunia2.ConvertBinaryObject.exe like you did with entitylibrary.fcb. When done modifying those files drag it back over the exe and it will repack the file but give it the .fcb extension. Just rename the extension to what it's supposed to be.
Also if you make changes from common.dat/fat or fc3_main.fat/dat DON'T repack your changes into those files. Just make the corresponding directory in patch_unpack and do it that way.
For merging mods just make sure you carefully copy the directory structure or it won't work.
For unpacking fc3_main.fat/dat you'll want to have Gibbed's tools in your main C:/ or whatever your drive is directory. The reason is the tool crashes when dealing with that file when in other directories (maybe not always, but it does for me).
I hope that helped you or anyone else that has had trouble creating or merging mods.
if you want to learn know how to hex edit to holster your weapon see here.