Usually what I do is this....Use this script to launch my HS Script.
Then as I use RL (works with HLHQ too) to create profiles for HS and RL and any others I require.
What happens:
Script launches and sets xpadder to use HS script. Select game or system. RL loads appropriate system/game xpadder profile. Upon exiting emulator RL loads blank xpadder profile and then HS profile and the loop continues. You must setup keymapper to xpadder in RL to get this to work.
Note: this v1.08 does have xbox360 controller support however I found that some buttons didn't work properly but xpadder profiles launched from it worked good. Remember to turn off joysticks in the ini file if you decide to use xpadder otherwise you have 2 programs doing the same thing which isn't a good idea.