Sure, I can do that, but remember that I am a n00b at this as well, so it might not be the correct way or even intended this way =)
First: The downside! Doing it this way means you have to launch your emulators through HyperLaunch. If you start them manually or with any other launcher, the keys will be all wrong of course.
In HyperLaunchHQ, select your system you want to remap on the left.
Go to Settings and make sure "Ahk Method" is set to "Internal". This enables the whole thing.
Also in the Keymapper field, make sure the other settings are false.
So in other words:
JoyIds Enabled: false
Ahk Method: Internal
I have actually not used any other keymapper at the same time. Might work I guess =)
Still with your system selected, go to Keymapper
In the AutoHotKey tab (first one), click Add (green cross) if you want to make changes to all games for the whole system.
If you only want the settings for a particular game in that system, press the little arrow next the the green + and select "Game Profile" instead. Those changes will only be for that game that you select then.
If you use multiple emulators for the same system and only want the changes for a specific emulator, click the Emulator profile instead.
Now that we have created an AHK profile, select it in the list below.
You now have two ways to configure the remapping.
1: In the bottom field, just click the green plus and it will tell you how it works (basically, press original key and then press the key it should act as instead).
Keep pressing + for evey key.
2: Free edit mode. You can jump to this mode whenever you want. If you add a key with the first method first, you'll see how you should type it out manually (orgkey::newkey).
Even if you've used method one but want to change a key, switch to Free Edit Mode and edit or delete the key as you want.
When done, remember to click the "Save current Ahk profile" button that is only lit up in Free Edit Mode (and only needed in Free Edit Mode).
Some keys, of course, does not type anything when pressed, such as control. Just change out of Free Edit Mode and do the first method for it, then you'll see what you have to type for it ( remapping left control to n, for example, is LControl::n )
When you are finished, you can click the green lightning icon (test selected ...) at the top to test your settings.
Some things I've noticed with the x-arcade. Sometimes it shows a weird code instead, like vkA2sc01D::c. That seems to work as well, but its ugly as I have no idea what vkA2sc01D is. When that happens, I just switch to free edit mode, remove it and try again. Usually its correct on the second try.
Sometimes it works in HyperLaunchHQ but not in the emulator I start, or only some keys work. When this happens (only happened once or twice), I simply remove the profile and restart. That at least worked for me. Edit: See Edit2 at the end.
Now then, I guess you need to configure your new keys in the emulator. The problem is that if you start the emulator through HyperLaunch and make changes, they are not always saved. The guides say that you should configure your emulator outside of HyperLaunch, but how do you do that when your new keybindings are only in effect if you launch it through HyperLaunch?
1: Either just hit the new keys manually in the emulator but then you have to remember which keys you've remapped to what. Not always easy.
2: Go back to the KeyMapper and press the green lightning to test your settings. Now, the new keymappings are actually used EVERYWHERE while the test window is up, so while its up, start your emulator manually and do the keybindings.
If you want to setup the exact same keymappings for another system, you can copy the old settings in Free Edit Mode and just paste them into the other system (also in Free Edit mode).
Edit: This is the one I use for the SSF (Sega Saturn Emulator) as its kinky as hell on which buttons work.
; One / Two Player buttons
; Joy 1 directions.
; Joy1 buttons
; Joy 2 directions
; Joy 2 buttons.
Edit2: One last thing. I dont know if this is a bug or not. You can NOT remap keys set as your "Exit Emulator key". If you have, say "a" as an exit key, you can not remap it. Also seems that you can not set a different exit key per system, only global, so do not try to remap any keys that you use as an exit key right now.