A lot of people find it easier to write and keep their ideas flowing when they are writing by hand. Unfortunately, as you suggest, that makes it difficult to rearrange the order in which your ideas get written down. If you decide to introduce a character earlier in the story or if you decide you need to provide more information to an earlier portion of the story it becomes a problem.
What I tend to do is just keep writing, without consideration of where everything need to fall into place. I will usually write comments in the margins to help me remember what I want to do with a new portion of text, and that often helps. In addition to this, I make sure I number my written pages so that I have a point of reference, and I will also number different sections of a story. For example, if I am writing a particular scene, I will draw a line in the margin to identify where that scene starts, and then I draw another line at the end of the scene. Then I can go back later and number the scenes. If I find myself adding content that needs to be placed elsewhere, I can refer to the page/section number to make it easier to organize when I start typing everything up.
Generally, I always write with an outline so that I can at least have a basic structure to start with. My outlines are usually numbered as well, so I may choose to refer to the outline numbering instead. Either way, as long as you can find a process that makes you comfortable and helps you to keep track of things, that's all that matters.
When I do start typing everything up, I will usually go through and read the handwritten copy first. At this time I will usually verify that my sections are numbered in the order in which I want them to appear by using red ink to number each section. That way if I have a section at the end of my handwritten copy that I wanted to appear earlier in the story, I can place it there as I'm typing to simplify the editing process later.