Perhaps you should tell us what the problem is exactly? The readme may be messy but it does tell you everything you need.
To simplify things I would recommend you concentrate on the WHDLoad set.
1. Download the WHDLoad set from
here. Extract them somewhere (Eg. C:\Roms\Amiga)
2. Download WinUAE Loader from
here.
3. Extract the WinUAELoader folder somewhere (Eg. C:\Emulators\WinUAELoader)
4. Downlaod the WinUAE emulator from
here. Extract is somewhere (Eg. C:\Emulators\WinUAE)
5. Run WinUAELoader.exe and set the paths (All you need to set are the "WinUAE Exe" to point to the emulator and "WHDLoad Games" to point to your games (Eg. C:\Emuators\WinUAE\WinUAE.exe and C:\Roms\Amiga respectively)
6. Test a game by going to Tools->Run Game "WHDLoad". Select a game and run it.
7. To run a game from your FE you need do it in the following format
WinUAELoader.exe -mode whdload -game "[ROM]"
Replace [ROM] with the variable your FE uses to send the game name. Eg. GameEx uses [ROM] and MaLa uses %Path%%ROM%%EXT%.
NOTE: You will also need the Kickstart ROMs in the correct place but I cannot tell you where you can get them from. As per the readme...
You need to place the Kickstart ROMs into WinUAELoader\WHD\Devs\Kickstarts (these are not included)
Copy them to WinUAELoader\WHD\Devs\Kickstarts\ and rename them as follows
kick34005.A500 <-- Actual ROM (Kickstart v1.3 rev 34.5 (1987)(Commodore)(A500-A1000-A2000-CDTV).rom)
kick34005.A500.RTB
kick40068.A1200 <-- Actual ROM (Kickstart v3.1 rev 40.68 (1993)(Commodore)(A1200).rom)
kick40068.A1200.RTB
kick40068.A4000 <-- Actual ROM (Kickstart v3.1 rev 40.68 (1993)(Commodore)(A4000).rom)
kick40068.A4000.RTB
You also need to have them setup correct for WinUAE (the emulator).