How do you update recipes?

kellybones

So, I found this recipe that I like:
http://allrecipes.com/Recipe/Savory-Sausage-Cheese-and-Oat-Muffins/Detail.aspx

Savory muffins! Sound good, right?

But my question is, how do you switch out and update recipes to what you have on hand or what you are willing to use?

Like, I would like change the all purpose flour with as much whole wheat flour as possible. Can you just exchange one-to-one?
I'd also like to swap out the garlic powder and onion powder for fresh garlic and onions. And to swap the reduced-calorie margarine for olive oil....

So apparently I want to change a lot of things! But, would you just go for it? Or is there a better way to do it?