Hey there!
With so many different dancing backgrounds coming into this community, you can see quite the showcase of different choreographing styles. A lot of people here use "combos," which is a couple or a series of moves strung together, which appear to have a particular flow.
Other people choreograph by counts- this spin takes four counts, this one takes two, hold this for four, and then can then create a dance to their music using the counts of the music as well. This is a more old-style approach, but I know that it has helped me to think about, and it's been useful for many people who've learned things like ballet, jazz and contemporary dance.
Otherwise, it helps to listen to the music you like and choose a song to choreograph to. Depending on what it is you focus on when listening to the music (lyrics, beat, etc.) you can tailor your dance to that.
From that, you can decide where you'd like some things to go. A slower point in the song is often a good time (for some people) to do floorwork or certain types of aerial moves, and faster paces are good for spins and more energetic movements.
Then again, if you like the lyrics, you can try to express those lyrics through your movement, depending on how you interpret what each move is "saying."
Really, it's up to you "how" you do it, and you will find that your style and ability changes over time and with experience. This is how an artistic endeavor goes!
Main thing though: Practice. It will help you memorize routines you've come up with, help you "feel" your music (which can lead to subtle, or not-so-subtle changes in your dance) and allow you to feel confident with the movements.
On the topic of combos: You'll find those happen sometimes at random, which is why many people enjoy taping their free-dancing time. Suddenly you'll do something and think "Wow, that was cool!" and often, by the end of your workout, you can't remember it anymore. I know that's happened to me!