Filtering mail before your Rules allows the Junk Mail filter to use those emails to continue learning and improving it's results. Filters/Rules take action based on the first match, so either the Junk mail filter matches first or your Rules match first. It's your preference. It will never match both. That's just not how these things work. Also note that the order of your Rules themselves has a bearing on the results. Let's say you want to move all emails with "Humor" in the subject to a certain folder, but you dislike emails with a subject of "Viagra Humor". You'd then want to make sure your "Viagra" rule is above your "Humor" rule on the list to make sure it gets rid of it before sending it to your "Humor" folder.
