You might get the best advice by writing directly to the recipe's author: http://food52.com/users...
Click on the envelope icon.

Nicole,
Active dry yeast has to proof, or "rise" as you described it; whereas the instant (or bread machine) variety does not and can be added with the rest of the dry ingredients without the extra step of proofing. The active stuff is a slightly different animal than the instant, as it needs some warm (not hot) water and a little sugar to get woken up. I've found that distilled water, instead of water straight out of the tap works best for proofing yeast, as the chlorine from municipal water can kill the yeast. Even if you have a very good well, distilled water can change your baking life. And don't buy distilled water. Put twice the amount of water you need for the recipe, and bring to a rapid boil, uncovered for twenty minutes. Voila! Pure H20. Proof your yeast when the water reaches 110-120 degrees fahrenheit, and let the rest continue to cool for use in your final product.

As to the difference between Brown and Granulated sugars, I'm not entirely sure what you mean as it applies to this recipe. However, I can tell you that brown sugar is packed in molasses and the granulated stuff (I assume you mean white) is refined, and bleached to within an inch of its existence. I never use white sugar, always raw. Which has the brown-ish color of brown sugar, because it has not been bleached, and is minimally processed (or so I'm told). As far as the cinnamon roll recipe is concerned, if you plan on using brown instead of granulated sugar, look up a substitution. Also be aware that the molasses in the brown sugar will caramelize a lot faster than the sugar itself and certainly the white sugar. So, you could end up with cinnamon rolls of significantly darker color, or worse something burnt. Maybe.

In my experience a person never really knows how to make something -especially something as fickle as a bread- until they've done it at least a dozen times.

Thanks Michael! I assumed that even though the recipe did not include the step of letting the yeast poof that it probably would not turn out well without doing so. Is there a drawback of using instant yeast in place of active/traditional yeast in cinnamon rolls or other bread recipes? With regards to the sugar, I was in fact referring to the filling and how the end result would turn out using brown sugar instead of white bleached granulated sugar. I have just always know cinnamon rolls that have been made with brown sugar so it made me a bit curious. Thanks so much for answering my questions and I will definitely use your tips about distilled water and raw sugar when I try this one again!

Any time a recipe calls for active yeast, you do have to proof it. I think that's a step that gets left out because some of us just assume that proofing yeast is one of those "duh" things... Arrogant on the part of those of us who've been baking for years, and downright detrimental if you don't know that you're dealing with an entirely different animal.
Actually, I've never used the instant yeast; so I can't speak to advantages or disadvantages of the stuff, and I've never used a bread maker. I WAS the bread maker when I was growing up. :) I learned with the active dry, so that's all I've ever used. When the recipe calls for instant, I use the active and just reduce the wet ingredients and add it judiciously until the dough I have in my hands "feels right" ... Yes, that's entirely ambiguous, and I have no way to describe it in measurable terms. Years of trial, error, and criticism from my grandmother is how I learned to get it right by feel alone. A route I recommend for anyone, but not if you're planning on enjoying it.