While @DTP's answer is accurate, I'd like to point out a few things.
The difficult part is my writing style revolves around a confusing and mysterious character.
I have no intention to be mean, but if this question is an example of your writing style, then it clearly shows a problem of clarity. I strongly advise you to use your words more carefully in your next question (if you don't decide to edit this one). If English is not your native language, I suggest that you use shorter sentences and respect when to use capital letters.
The sentence above is confusing: what is the problem exactly? Is it your writing style or the plot/book which revolves around the mysterious character?
I can only suggest that you analyse your main plot and your mysterious character, then make your writing as clear as you can.
It's not choppy but it's missing pieces.
I'm afraid I'll have to disagree: if it's missing pieces, it's choppy. Missing pieces means that the action doesn't flow gracefully, which means there are hiccups in the flow and that is aptly described by the word 'choppy'.
I need to fill the book with 'fluff'.
No, you don't. Nobody does. Fluff is what gets edited out, not edited in.
I need to fill the book with [...] parts that glue the story together but aren't particularly important.
I'll assume that by 'not particularly important' you mean 'less important' rather than 'inconsequential'.
If your problem is a choppy main plot, there are two things you must do:
1: analyse your main plot and discover why it is choppy in the first place.
2: if the choppiness is derived from a lack of secondary plots that help attain a greater sense of unity, then focus on creating said plots in a way that build up the main one.
I'm going to go out on a limb and guess that what you're thinking of when you say 'fluff' and 'not particularly important' is character development. If I'm correct, let me say that character development should not be fluff (and if it happens to be, then it should be edited out without delay) and is definetely not 'not particularly important'.
Character development is what will make your reader relate to the characters. In other words, it's what will give the reader a reason to stick till the end of the story, so yes, it is important. If your main plot does not give the opportunity for sufficient character development, then create secondary plots that serve both the sequence of events of the main plot as well as character development.
Just to make sure this is hitting home, think about a story as a lasagna: the main story is the pasta (if you don't have pasta, it's not lasagna, no matter if everyhting else is the same). The things that glue the lasagna together - the meat (or vegetables) and the sauce - those are the 'fluff' you're asking about. Would you eat lasagna without that 'fluff'? No, because it isn't fluff: what glues the main story together and brings it to life is just as important as the main story itself. It's what gives it flavour and makes it remarkable.
How do I do this without combating with my story line?
You don't want to fight your main story line; you want to create supporting story lines and develop your characters in a way as to make the main story flow without hiccups.
I'm writing a book and I'm finished but it is way to short.
Lastly, I'd suggest you don't think about length. The important thing is that the story flows - the main plot with the secondary-supporting plots, both giving the characters the opportunity to grow and mature. It is not important if it's 10,000 or 100,000 words long.