IMPORTANT! If you are having "Melee" action fire when you move the right-joystick, that means you used Input files [unpatched version]
instead of Input files [latest version] like you needed to use for your version. Read the instructions next to STEP A below again and copy the correct files.
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Edits:
Note: Re-copy the files from [R3H4B] BFBC2_Nopad.zip after patching to a newer version of the game and don't restore control defaults or change keymappings.
Note: this profile requires Pinnacle v5.7.0 or higher!
!! TO REMOVE THE DEFAULT JOYPAD CONFIG AND TO FIX TRIGGER ISSUES (WHICH IS NEEDED FOR THE PROFILE TO WORK) DO THE FOLLOWING (STEP A and B)!!
A ) After game installation, extract the files included in the [R3H4B] BFBC2_Nopad.zip file to:
in "My documents"
1: Go to "My Documents"- folder (Start->"Documents" or "MyDocuments" ) and look for "BFBC2".
2: If the "BFBC2"-folder is missing, start the game once and exit out of the game or just create it manually in your "My Documents" folder.
3: Get into the "BFBC2"-folder. Check here for a folder called "Input". If the "Input"-folder is missing, just create it manually.
4: If the "Input"-folder already exists, remove its contents and extract the files from [R3H4B] BFBC2_Nopad.zip (* from the corresponding folder, see below) into the "Input"-folder.
*=Inside the .zip you'll find two folders:
- Input files [latest version]
- Input files [unpatched version]
Because the files are depending on which version of the game you have, it's very important to choose the files from the correct folder. So if you're using the unpatched version, use the files from "Input files [unpatched version]" and copy them to your "input"-folder. If you have updated your game to the latest version, use the ones from "Input files [latest version]".
You can verify if this worked by going into the game's options. The joystick controls should all be empty! (unpatched version)

B) After importing the profile, Battlefield Bad Company 2 - R3H4B's profile.pin, Enable "game hook" by going to the "Game profiles"-screen->"edit.."->"Advanced"-tab->"Install now" (lower left corner); OK save and close

Optionally: If you still have the main menu popping up when clicking the right thumbstick button:
Find out where your games' main executable resides (BFBC2Game.exe) Something like:
C:\Program Files\Electronic Arts\Battlefield Bad Company™ 2\BFBC2Game.exe
If you can find it, please extract the contents of the following file to it:
Put in game directory.zip
So make sure the three files from the zip are in the exact same folder as the game's main executable and start the game. If done correctly, the game shouldn't be able to detect your joypad and your rightstick button should work.
To sum it up, do in the following order:
1. Install the game and apply patches/update the game to the latest version. Start the game and exit.
2. Open [R3H4B] BFBC2_Nopad.zip and choose the input files applicable to your version of the game. (so if you updated, choose Input files [latest version]). Copy the files to the BFBC2/Input directory in MyDocuments as described above.
3. Import the profile, Battlefield Bad Company 2 - R3H4B's profile.pin.
4. Enable "game hook" by going to the "Game profiles"-screen->"edit.."->"Advanced"-tab->"Install now" (lower left corner); OK, save and close
5. Optionally: disable menu on right stick button-issue by extracting these files to game directory Put in game directory.zip
6. Optionally: Disable Mouse Smoothing if you have out of sync problems
Edit: just try steps 1-4 first. Only perform step 5 if 1-4 are successful and the game works with the settings/profile and you have sync problems!
The layout is the same as the X360-version of the game:

Or check the Pinnacle layout here: [R3H4B] Battlefield - Bad Company 2 Layout.pdf
Check here for the X360-layout:
http://www.allgame.com/game.php?id=68550&tab=controls
Errol contributed a very useful instruction on how to remove the game's Mouse Smoothing, making the controls a lot more responsive:
BFBC2 Disable Mouse Smoothing.zip
Thanks Errol!
For "aim down sights" on trigger pull/release or crouch toggle update the game to latest version and use the toggles in the option menu.
The commands are also in the profile but please use the game's toggles if possible. Only use the ones in the profile if you have the unpatched version of the game.
Steam settings (32-bit Windows):
Code:
Launch file: "C:\Program Files\Steam\steam.exe" -applaunch 24960
Detect file: C:\Program Files\Steam\SteamApps\common\battlefield bad company 2\BFBC2Game.exe
Work path: C:\Program Files\Steam\SteamApps\common\battlefield bad company 2\
Hook path: C:\Program Files\Steam\SteamApps\common\battlefield bad company 2\
Happy gaming and feedback is always appreciated!
Hope you like it.