You will need all the files in your FPGAMING Directory, or the Original Disk (Depending on which games you will be playing). Do not forget that if you are playing QUAKE on someone else's machine it may need to be patched (to Version 1.6) and you will need to copy the assassin.cfg to the ..\QUAKE\ID1 Directory.

If you are just playing DOS Quake you might just make a special disk with,
ASSASSIN.EXE the Calibration and test Program.
ALAUNCH.EXE the Launch program for the Assassin 3D.
ASSASSIN.INI the Calibration information..
ASSASSIN.CFG your Quake button bindings.
QUAKE.INI used by alaunch to configure Quake.
DOS4GW.EXE used by alaunch.exe and assassin.exe
Q101-106.ZIP the patch file to upgrade Quake from Ver 1.01 to 1.06.
The remaining ????????.INI files if you are going to play other games.

Then copy all files to the ..\QUAKE Directory, Move the ASSASSIN.CFG to the ..\QUAKE\ID1 Directory. And from your ..\QUAKE> prompt type

SET FPGAMING=C:\QUAKE <--Presuming that is the correct directory.

You will want to run ASSASSIN.EXE to Calibrate and Test the Assassin 3D and Joystick.
Then the normal ALAUNCH QUAKE.

NOTE: If you are going to be playing a Windows version of Quake you will need to install the Windows Direct Input Drivers as well. Windows Driver Page This file includes the Windows and Dos Drivers. Do not forget your edited ADVA3D.CFG file.