Keith, the flattening of your file will occur in the printstream - in other words, when you print the file, the data is flattened as it is sent to your RIP. So, you most likely don't need to "pre-flatten" unless you are running into a problem on a certain job.
Having spent a lot of time understanding how effects get flattened before I eventually moved to an APPE workflow, I can tell you that the easiest thing to do is to get to know the Flattener Preview in Illustrator and InDesign. You can use it to (a) see what objects are transparent and (b) see how the flattening of those transparent objects will affect underlying and surrounding objects.
Armed with this info, you have a much better idea of where your problems are likely to be in the printed piece. You can also use the info to make preemptive decisions to minimize what gets flattened. The most important thing to remember is that flattening occurs from the transparent object down (anything that lives below the transparent object in the stacking order will be affected by flattening.) To protect an object from unwanted flattening, bring it to the front of the stacking order (layers are helpful for this, but a simple "bring to front" will do the trick.) A common scenario is that a picture has a drop shadow, and the caption under the picture has type that gets fattened during flattening. This occurs because the drop shadow lives above the caption in the stacking order, so the caption gets partially rasterized and so looks fatter. But, bring the caption above the drop shadow in the stacking order and now the caption is protected from flattening.
