The software just helps you crunch the numbers. You visualize the beer, brew the beer, taste the beer, and adjust the recipe accordingly.
Its more important to figure out how to get what you want out of your ingredients and process. What good is your own recipe if the resulting beer isn't what you wanted?
When I started branching out from kits, I would brew one kit several times, tweaking one ingredient at a time. This way, you can learn what individual ingredients bring to a beer while being fairly confident the result will be worth drinking. You can also start learning the software this way. Input the kit ingredients into a recipe and explore a change before brewday.
If you're brave, you can brew a beer with one malt (or type of malt extract), one hop, and one type of yeast. Then, brew the beer again, and add a steeping grain, or change the type of base malt (extract), and see how the beer changes. IMO this is the best way to learn ingredients, but its tough to commit to one type of beer!
Either way - its a fun time in your journey as a homebrewer! Embrace it and dive in!