There is a good chance flirc will work out of the box to wake up your machine when a remote button is pressed. However, if this is not the case, you've come to the right place.
Download and install the latest GUI (see here for instructions)
Once you've gotten the latest GUI, open the app and select "Full keyboard controller"
Now click and pair the 'wake' button on the keyboard view with the button on your remote you want to use to wake up your machine.
Okay, you are almost done! Don't forget the last step, it's important. Now that this button is paired, let's enable the feature in flirc.
Head on over to the advanced configuration window:
Now, whenever that previously paired button 'wake' has been pressed, a special wake up command will be sent to your machine only when your computer is sleeping.