Sixburg,
What you need to watch out for is placing any boxes on signal you want to keep, especially if it is a weak signal such as faint nebulosity or faint galaxy arm features. If in doubt, remove any boxes so that the process does not treat the signal as something to be corrected. In other posts Juan and other pros have suggested that you minimize boxes by just placing a few. Another good guide is Harry's tutorials that have one specifically on using the DBE and is the process I follow most of the time.
As to seeing whether you are removing data, that will not become evident until much later in the process workflow when you go to bring out all the faint stuff so just flipping between two DBE products may not show what you have lost.
When I use DBE on binned image stacks I usually set the "generate matrix" settings at around 12/20/0.375 and then delete any that threaten areas of signal. I usually up the first setting to around 20 for unbinned imager stacks. Note, if you haven't discovered it yet, its easy to delete a whole set of boxes in a column by clicking on the top one you want to delete and just repeatedly hitting delete until you are done with that column (probably obvious, but it took me a while to find that shordut so I'm passing it along).
Hope that helps,
Jim