I spend many hours trying to find some tutorial or manual that explain how to use HIP but coulnd find it, i get frustrated many many times when things doesnt work but finally i completly understand HIP at least for MCE remote, so i'll write this little guide and hope it helps you.
First of all do what says here.:
http://www.byremote.com.au/Hip/mce_remote_faq.htm
This are the basics of the work and the developer nows the best just do what he sais.
The when you get HIP running is pretty simple if you want to make the remote launch any program or command just go to File/preferences/alternate input, under the system-wide keys window you'll see some command and buttons just click add value, press the key you want to config on your remote and then select what you want it to do, you can select from several predefined options, add programs or keyboar options.
Now you set some apps to open with your remote, i use it to make it lauch WinTv.
Now the interesting part, how to make work with any other divece that use remote.
You have to open the HIP configuration window and the go to Remote I/O/Edit IR Commands
In this window you'll teach HIP the commands from the other remote you want to MCE remote control, so you and every key you want to use, push Add IR, learn IR directly from a remote control and push the button you it to learn, careful cause it learn the time you push the button so one quick touch is enough.
Set all the buttons you want.
Then go to the config window of HIP
And add the program you want to use the commands, i add wintv cause i want to control my STB with my remote.
Then you just have to Add value like the first time, to use the IR codes learn just push the keyboard icon next to the Primary command box, and push Send IR, select the command you want to send and you're done.
If you want it to send a command on any app just add it in the prefererence/alternate input option. The values entered on config windows are for specific programs or app.
Hope it helps and sorry for some errors in typing, english is not my native language.