Using a rooted HTC One M7 and stock rom.
After days of messing around with settings this is what worked for me:
-download and install the latest .zip of SuperSU for your phone.
-uninstall sixaxis if you have it already, then re-install so its fresh (default settings)
-run sixaxis and find your phone's bluetooth address, 12 character eg. XX:XX:XX:XX:XX:XX
-download for your pc the pairing tool for pairing your ps3 controllers (these are the only ones I've tried)
-enter your phones address for each of the controllers that you plug in to you PC via usb
-Now open sixaxis, click start, then press the PS button on player one, wait for it to be recognised,
-Then click "Change IME" (below start) and select "sixaxis controller"
then press PS on controller 2 and wait for it to be recognised
-Go into preferences (3 dots top right) then gamepad settings and make sure "enable gamepad" is ticked.
-(leaving sixaxis running in background) open fpse and select the game you want to play.
-Then press any button (I use start) on controller one. Gamepad 1 and Gamepad 2 should show,
select gamepad 1
-Press any button on controller 2 and select gamepad 2.
-That's itAdditional stuff:
-to change what buttons on each controller do what, it will always be in the emulator NOT sixaxis
-For FPSE go into:
settings- gamepad- buttons mapping- Assign Hw keys fors Pad 1/2/3/4.
Tap on button listed then press on controller the one you would like it to be.
-Tekken 3 was really annoying me, then realised I had to go into versus,
it wouldn't let player 2 join from the arcade selection, so be aware of this in other games too!
Hope this helps someone. Loads of appreciation for both of these apps and their creators.