If you select the IEH output formats, the footnotes are already included since these output options just reconstruct the IEH for various conditions. Please note that based on the complexity and data quantity, the extraction can take a long time. The processing power of your computer is also a factor. You might consider setting up smaller queries to adjust your output data using a single year, then go to larger queries you can let run overnight. Until you become more familiar with this program, I suggest doing smaller queries and examining the output before committing to large span queries.
Suggestions are be sure to setup the data and exe directories properly.
You can use the IEH from cd but be sure the output directory is on a writeable disk. Word of caution - this program is beta, it has evolved since it was first designed and is fairly complex so results can vary. I've tried most of the general queries I can think of and they work pretty well. Please record any queries you attempt that produce odd results or crash the program.