Quite often when people are working on materials for their Blackboard course sites the documents that they want use already exist as Micrsoft Word documents so the tendency is to copy and paste from that document into the Blackboard text editor. When you do that Word makes its own HTML and the result when the document goes into Blackboard does not always look the way that it did when you created it. You may find things misaligned, unformated, no margins and in general looking very disorganized. This does not happen 100% of the time but it occurs quite frequently.
Now I would never suggest walking away from using Word to do the documents for your course, I would however suggest that once you have finished and saved it as a Word document (.doc or docx) that you also save the document in a format that will be more digestible for Blackboard. When you select Save As in the File Menu (2003) or from the Office Button (2007) you will get a pop up window that will ask you what location you want to save to and the bottom most drop down will allow you to save the document in a different file format. I would reommend plain text (.txt) this will allow for a smooth transition into Blackboard and you can then make any formatting changes with the aid of the tools provided in the text editor.